Non-a, non-b, non-c, non-c, non-d, non-e hepatitis reagents and methods for their use

ABSTRACT

Hepatitis GB Virus (HGBV) nucleic acid and amino acid sequences useful for a variety of diagnostic and therapeutic applications, kits for using the HGBV nucleic acid or amino acid sequences, HGBV immunogenic particles, and antibodies which specifically bind to HGBV. Also provided are methods for producing antibodies, polyclonal or monoclonal, from the HGBV nucleic acid or amino acid sequences.

This application is 371 of PCT/US95/02118, filed Feb. 14, 1995 and acontinuation-in-part application of U.S. Ser. No. 08/377,557 filed Jan.30, 1995, abandoned which is a continuation-in-part of U.S. Ser. No.08/344,185 filed Nov. 23, 1994 abandoned and U.S. Ser. No. 08/344,190filed Nov. 23, 1994, abandoned which are each continuation-in-partapplications of Ser. No. 08/283,314 filed Jul. 29, 1994, abandoned whichis a continuation-in-part application of U.S. Ser. No. 08/242,654, filedMay 13, 1994, abandoned which is a continuation-in-part application ofU.S. Ser. No. 08/196,030 filed Feb. 14, 1994, abandoned all of whichenjoy common ownership and each of which is incorporated herein byreference.

BACKGROUND OF THE INVENTION

This invention relates generally to a group of infectious viral agentscausing hepatitis in man, and more particularly, relates to materialssuch as polynucleotides derived from this group of viruses, polypeptidesencoded therein, antibodies which specifically bind to thesepolypeptides, and diagnostics and vaccines that employ these materials.

Hepatitis is one of the most important diseases transmitted from a donorto a recipient by transfusion of blood products, organ transplantationand hemodialysis; it also can be transmitted via ingestion ofcontaminated food stuffs and water, and by person to person contact.Viral hepatitis is known to include a group of viral agents withdistinctive viral genes and modes of replication, causing hepatitis withdiffering degrees of severity of hepatic damage through different routesof transmission. In some cases, acute viral hepatitis is clinicallydiagnosed by well-defined patient symptoms including jaundice, hepatictenderness and an elevated level of liver transaminases such asaspartate transaminase (AST), alanine transaminase (ALT) and isocitratedehydrogenase (ISD). In other cases, acute viral hepatitis may beclinically inapparent. The viral agents of hepatitis include hepatitis Avirus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitisdelta virus (HDV), hepatitis E virus (HEV), Epstein-Barr virus (EBV) andcytomegalovirus (CMV).

Although specific serologic assays available by the late 1960's toscreen blood donations for the presence of HBV surface antigen (HB sAg)were successful in reducing the incidence of post-transfusion hepatitis(PTH) in blood recipients, PTH continued to occur at a significant rate.H. J. Alter et al., Ann. Int. Med. 77:691-699 (1972); H. J. Alter etal., Lancet ii:838-841 (1975). Investigators began to search for a newagent, termed “non-A, non-B hepatitis” (NANBH), that caused viralhepatitis not associated with exposure to viruses previously known tocause hepatitis in man (HAV, HBV, CMV and EBV). See, for example, S. M.Feinstone et al., New Engl. J. Med. 292:767-770 (1975); Anonymouseditorial, Lancet ii:64-65 (1975); F. B. Hollinger in B. N. Fields andD. M. Knipe et al., Virology, Raven Press, New York, pp. 2239-2273(1990).

Several lines of epidemiological and laboratory evidence have suggestedthe existence of more than one parenterally transmitted NANB agent,including multiple attacks of acute NANBH in intravenous drug users;distinct incubation periods of patients acquiring NANBHpost-transfusion; the outcome of cross-challenge chimpanzee experiments;the ultrastructural liver pathology of infected chimpanzees; and thedifferential resistance of the putative agents to chloroform. J. L.Dienstag, Gastroenterology 85:439-462 (1983); J. L. Dienstag,Gastroenterology 85:743-768 (1983); F. B. Hollinger et al., J. Infect.Dis. 142:400-407 (1980); D. W. Bradley in F. Chisari, ed., Advances inHepatitis Research, Masson, N.Y., pp. 268-280 (1984); and D. W. Bradleyet al., J. Infect. Dis. 148:254-265 (1983).

A serum sample obtained from a surgeon who had developed acute hepatitiswas shown to induce hepatitis when inoculated into tamarins (Saguinusspecies). Four of four tamarins developed elevated liver enzymes withina few weeks following their inoculation, suggesting that an agent in thesurgeon's serum could produce hepatitis in tamarins. Serial passage invarious non-human primates demonstrated that this hepatitis was causedby a transmissible agent; filtration studies suggested the agent to beviral in nature. The transmissible agent responsible for these cases ofhepatitis in the surgeon and tamarins was termed the “GB agent.” F.Deinhardt et al., J. Exper. Med. 125:673-688 (1967). F. Deinhardt etal., J. Exper. Med., supra; E. Tabor et al., J. Med. Virol. 5:103-108(1980); R. O. Whittington et al., Viral and Immunological Diseases inNonhuman Primates, Alan R. Liss, Inc., New York, pp. 221-224 (1983).

Although it was suggested that the GB agent may be an agent causingNANBH in humans and that the GB agent was not related to the known NANBHagents studied in various laboratories, no definitive or conclusivestudies on the GB agent are known, and no viral agent has beendiscovered or molecularly characterized. F. Deinhardt et al., Am. J.Med. Sci. 270:73-80 (1975); and J. L. Dienstag et al., Nature264:260-261 (1976). See also E. Tabor et al., J. Med. Virol., supra; E.Tabor et al., J. Infect. Dis. 140:794-797 (1979); R. O. Whittington etal., supra; and P. Karayiannis et al., Hepatology 9:186-192 (1989).

Early studies indicated that the GB agent was unrelated to any knownhuman hepatitis virus. S. M. Feinstone et al., Science 182:1026-1028(1973); P. J. Provost et al., Proc. Soc. Exp. Biol. Med. 148:532-539(1975); J. L. Melnick, Intervirology 18:105-106 (1982); A. W. Holmes etal., Nature 243:419-420 (1973); and F. Deinhardt et al., Am. J. Med.Sci., supra. However, questions were raised regarding whether the GBagent was a virus which induced hepatitis infection in humans, or alatent tamarin virus activated by the GB serum and once activated,easily passaged to other tamarins, inducing hepatitis in them. Also, asmall percentage of marmosets inoculated with GB-positive serum did notdevelop clinical hepatitis (4 of 52, or 7.6%), suggesting that theseanimals may have been naturally immune and thus, that the GB agent maybe a marmoset virus. W. P. Parks et al., J. Infect. Dis. 120:539-547(1969); W. P. Parks et al., J. Infect. Dis. 120:548-559 (1969).Morphological studies have been equivocal, with immune electronmicroscopy studies in one report indicating that the GB agent formedimmune complexes with a size distribution of 20-22 nm and resembling thespherical structure of a parvovirus, while another study reported thatimmune electron microscopy data obtained from liver homogenates ofGB-positive tamarins indicated that aggregates of 34-36 nm withicosahedral symmetry were detected, suggesting that the GB agent was acalici-like virus. See, for example, J. D. Almeida et al., Nature261:608-609 (1976); J. L. Dienstag et al., Nature, supra.

Two hepatitis-causing viruses recently have been discovered andreported: HCV, which occurs primarily through parenteral transmission,and HEV, which is transmitted enterically. See, for example, Q. L. Chooet al., Science 244:359-362 (1989), G. Kuo et al., Science 244:362-364(1989), E. P. Publication No. 0 318 216 (published May 31, 1989), G. R.Reyes et al., Science 247:1335-1339 (1990). HCV is responsible for amajority of PTH ascribed to the NANBH agent(s) and many cases of acuteNANBH not acquired by transfusion. Anonymous editorial, Lancet335:1431-1432 (1990); J. L. Dienstag, Gastroenterology 99:1177-1180(1990); and M. J. Alter et al., JAMA 264:2231-2235 (1990).

While the detection of HCV antibody in donor samples eliminates 70 to80% of NANBH infected blood in the blood supply system, the discoveryand detection of HCV has not totally prevented the transmission ofhepatitis. H. Alter et al., New Eng. J. Med. 321:1494-1500 (1989).Recent publications have questioned whether additional hepatitis agentsmay be responsible for PTH and for community acquired acute and/orchronic hepatitis that is not associated with PTH. For example, of 181patients monitored in a prospective clinical survey conducted in Francefrom 1988 to 1990, investigators noted a total of 18 cases of PTH.Thirteen of these 18 patients tested negative for anti-HCV antibodies,HBsAg, HBV and HCV nucleic acids. The authors speculated as to thepotential importance of a non-A, non-B, non-C agent causing PTH. V.Thiers et al., J. Hepatology 18:34-39 (1993). Also, of 1,476 patientsmonitored in another study conducted in Germany from 1985 to 1988, 22cases of documented cases of PTH were not related to infection with HBVor HCV. T. Peters et al., J. Med. Virol. 39:139-145 (1993).

It would be advantageous to identify and provide materials derived froma group of novel and unique viruses causing hepatitis, such as,polynucleotides, recombinant and synthetic polypeptides encoded therein,antibodies which specifically bind to these polypeptides, anddiagnostics and vaccines that employ these materials. Such materialscould greatly enhance the ability of the medical community to moreaccurately diagnose acute and/or chronic viral hepatitis and couldprovide a safer blood and organ supply by detecting non-A, non-B andnon-C hepatitis in these blood and organ donations.

SUMMARY OF THE INVENTION

The present invention provides a purified polynucleotide or fragmentthereof derived from hepatitis GB virus (HGBV) capable of selectivelyhybridizing to the genome of HGBV or the complement thereof, whereinsaid polynucleotide is characterized by a positive stranded RNA genomewherein said genome comprises an open reading frame (ORF) encoding apolyprotein wherein said polyprotein comprises an amino acid sequencehaving at least 35% identity, more preferably, 40% identity, even morepreferably, 60% identity, and yet more preferably, 80% identity to anamino acid sequence selected from the group consisting of HGBV-A, HGBV-Band HGBV-C. Also provided is a recombinant polynucleotide or fragmentthereof derived from hepatitis GB virus (HGBV) capable of selectivelyhybridizing to the genome of HGBV or the complement thereof, whereinsaid nucleotide comprises a sequence that encodes at least one epitopeof HGBV, and wherein said recombinant nucleotide is characterized by apositive stranded RNA genome wherein said genome comprises an openreading frame (ORF) encoding a polyprotein wherein said polyproteincomprises an amino acid sequence having at least 35% identity to anamino acid sequence selected from the group consisting of HGBV-A, HGBV-Band HGBV-C. Such a recombinant polynucleotide is contained within arecombinant vector and further comprises a host cell transformed withsaid vector.

The present invention also provides a hepatitis GB virus (HGBV)recombinant polynucleotide or fragment thereof comprising a nucleotidesequence derived from an HGBV genome, wherein said polynucleotide iscontained within a recombinant vector and further comprises a host celltransformed with said vector and further wherein said sequence encodesan epitope of HGBV. The HGBV recombinant polynucleotide is characterizedby a positive stranded RNA genome wherein said genome comprises an openreading frame (ORF) encoding a polyprotein wherein said polyproteincomprises an amino acid sequence having at least 35% identity to anamino acid sequence selected from the group consisting of HGBV-A, HGBV-Band HGBV-C. The present invention provides a recombinant expressionsystem comprising an open reading frame of DNA or RNA derived fromhepatitis GB virus (HGBV) wherein said open reading frame comprises asequence of HGBV genome or cDNA and wherein said open reading frame isoperably linked to a control sequence compatible with a desired host,and further comprises a cell transformed with said recombinantexpression system and a polypeptide of at least about eight amino acidsin length produced by said cell.

The present invention additionally provides a purified hepatitis GBvirus (HGBV) comprising a preparation of HGBV polypeptide or fragmentthereof, a recombinant polypeptide comprising an amino acid sequence orfragment thereof wherein said sequence is characterized by a positivestranded RNA genome wherein said genome comprises an open reading frame(ORF) encoding a polyprotein wherein said polyprotein comprises an aminoacid sequence having at least 35% identity, more preferably 40% identityand yet more preferably 60% identity to an amino acid sequence selectedfrom the group consisting of HGBV-A, HGBV-B and HGBV-C. Antibodies, bothpolyclonal and monoclonal, are provided by the present invention, aswell as, a fusion polypeptide comprising at least one hepatitis GB virus(HGBV) polypeptide or fragment thereof, a particle that is immunogenicagainst hepatitis GB virus (HGBV) infection, comprising a non-HGBVpolypeptide having an amino acid sequence capable of forming a particlewhen said sequence is produced in a eukaryotic or prokaryotic host, andat least one HGBV epitope, and a polynucleotide probe for hepatitis GBvirus (HGBV) wherein said polynucleotide probe is characterized by apositive stranded RNA genome wherein said genome comprises an openreading frame (ORF) encoding a polyprotein wherein said polyproteincomprises an amino acid sequence having at least 35% identity to anamino acid sequence selected from the group consisting of HGBV-A, HGBV-Band HGBV-C.

Assay kits also are provided, as well as methods for producing apolypeptide containing at least one hepatitis GB virus (HGBV) epitopecomprising incubating host cells transformed with an expression vectorcomprising a sequence encoding a polypeptide characterized by a positivestranded RNA genome wherein said genome comprises an open reading frame(ORF) encoding a polyprotein wherein said polyprotein comprises an aminoacid sequence having at least 35% identity to an amino acid sequenceselected from the group consisting of HGBV-A, HGBV-B and HGBV-C. Alsoprovided are methods of detecting HGBV nucelic acids, antigens andantibodies in test samples, including methods which utilize solidphases, recombinant or synthetic peptides, or probes. Vaccines also areprovided by the present invention, as are tissue culture grown cellinfected with hepatitis GB virus (HGBV), a method for producingantibodies to hepatitis GB virus (HGBV) comprising administering to anindividual an isolated immunogenic polypeptide or fragment thereofcomprising at least one HGBV epitope in an amount sufficient to producean immune response. Diagnostic reagents also are provided herein whichcomprises polynucleotides or polypeptides or fragments thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1-12 are graphs of individual tamarins which plot the amount ofliver enzyme (ALT or ICD) as measured in mU/ml against time (weeks postinoculation), where ALT CO indicates the cutoff value for ALT, and ICDCO indicates the cutoff value of ICD, wherein

FIG. 1 shows the graph of tamarin T-1053;

FIG. 2 shows the graph of tamarin T-1048;

FIG. 3 shows the graph of tamarin T-1057;

FIG. 4 shows the graph of tamarin T-1061;

FIG. 5 shows the graph of tamarin T-1047;

FIG. 6 shows the graph of tamarin T-1042;

FIG. 7 shows the graph of tamarin T-1044;

FIG. 8 shows the graph of tamarin T-1034;

FIG. 9 shows the graph of tamarin T-1055;

FIG. 10 shows the graph of tamarin T-1051;

FIG. 11 shows the graph of tamarin T-1038; and

FIG. 12 shows the graph of tamarin T-1049.

FIG. 13 presents a flow diagram of the steps involved inrepresentational difference analysis (RDA), the procedure used foridentifying clones.

FIG. 14 shows an ethidium bromide stained 2.0% agarose gel of theproducts from the representational difference analysis (RDA) performedon pre-inoculation and acute phase HGBV-infected tamarin plasma.

FIG. 15 shows an autoradiogram from a Southern blot of genomic DNA,amplicon DNA and products from the first three rounds ofsubtraction/hybridization.

FIG. 16 shows the same autoradiogram as described in FIG. 15, exceptthat an alternative radiolabeled probe is used.

FIG. 17 shows an ethidium bromide stained 1.5% agarose gel of polymerasechain reaction (PCR) amplified product from genomic DNA.

FIG. 18 shows an autoradiogram from a Southern blot of the 1.5% agarosegel in FIG. 17.

FIG. 19 shows an ethidium bromide stained 1.5% agarose gel of RT-PCRproduct obtained from normal human serum and pre-inoculation and acutephase tamarin plasmas.

FIG. 20 shows an autoradiogram from a Southern blot of the same geldescribed in FIG. 19.

FIGS. 21A and B show autoradiograms from Northern blots of totalcellular RNA extracted from the liver of an uninfected tamarin and anHGBV-infected tamarin.

FIG. 22 shows a diagram that demonstrates each of the recombinantpolynucleotide isolates are present on contiguous RNA species.

FIGS. 23A-C show dot plot analyses of the nucleic acid sequenceswherein:

FIG. 23A shows a dot blot comparison of HGBV-A;

FIG. 23B shows a dot blot comparison of HGBV-B;

FIG. 23C shows a dot blot comparison of HGBV-A v. HGBV-B.

FIGS. 24A-B show the conserved residues as follows:

FIG. 24A shows the conserved residues in the putative NTP-bindinghelicase domain of predicted translation products of HGBV-A, HGBV-B andHCV-1 NS3,

FIG. 24B shows the conserved residues of the RNA-dependent RNApolymerase domain of predicted translation products of HGBV-A, HGBV-Band HCV-1 NS5b.

FIGS. 25A-B show Coomassie-stained 10% SDS-polyacrylamide gels of CKSfusion protein whole cell lysates; three CKS fusion proteins demonstrateimmunoreactivity with HGBV-infected tamarin sera.

FIGS. 26 to 30 are graphs of individual tamarins which plot 1) theamount of liver enzyme (ALT) as measured in mU/ml against time (weekspost inoculation) as shown by a solid line; 2) ELISA absorbance valuesfor the CKS-1.7 recombinant protein as shown by filled circles connectedby dotted lines; 3) ELISA absorbance values for the CKS-1.4 recombinantprotein as shown by open circles connected by dotted lines; 4) ELISAabsorbance values for the CKS4.1 recombinant protein as shown by crossesconnected by dotted lines; 5) negative PCR results using SEQUENCE I.D.NO. 21 primers as shown by empty squares; 6) postivive PCR results usingSEQUENCE I.D. NO. 21 primers as shown by filled squares; 7) negative PCRresults using SEQUENCE I.D. NO. 26 primers as shown by empty diamonds;8) positive PCR results using SEQUENCE I.D. NO. 26 primers as shown byfilled diamonds; 9) inoculation dates are indicated by the arrowheads,wherein

FIG. 26 shows the graph of tamarin T-1048;

FIG. 27 shows the graph of tamarin T-1057;

FIG. 28 shows the graph of tamarin T-1061;

FIG. 29 shows the graph of tamarin T-1051; and

FIG. 30 shows the graph of tamarin T-1034.

FIGS. 31-34 are graphs of a human test specimens which plots 1) theamount of liver enzyme (ALT) as measured in mU/ml against time (weekspost inoculation) as shown by a solid line; 2) ELISA absorbance valuesfor the CKS-1.7 recombinant protein as shown by dotted lines, filledcircles; 3) ELISA absorbance values for the CKS-1.4 recombinant proteinas shown by dotted lines, open circles, wherein

FIG. 31 shows a graph of patient 101;

FIG. 32 shows a graph of patient 257;

FIG. 33 shows a graph of patient 260; and

FIG. 34 shows a graph of patient 340.

FIG. 35 shows conserved residues, wherein

FIG. 35A shows the conserved residues in the putative NTP-bindinghelicase domain of predicted translation products of Contig. A, Contig.B and HCV-1 NS3, and

FIG. 35B shows the conserved residues of the RNA-dependent RNApolymerase domain of predicted translation products of Contig. A,Contig. B and HCV-1 NS5b.

FIG. 36 shows a nucleotide alignment of HGBV-A, HGBV-B, HGBV-C andHCV-1.

FIG. 37 shows a PhosphoImage (Molecular Dynamics, Sunnyvale, Calif.)from a Southern blot of the PCR products after hybridization with theradiolabeled probe from GB-C.

FIG. 38 shows a nucleotide alignment of HGBV-C with two variant clones.

FIG. 39 presents a schematic of the assembled contig of HGBV-C.

FIG. 40 shows a nucleotide alignment of HGBV-C with four variant clones.

FIG. 41 shows a PhosphoImage (Molecular Dynamics, Sunnyvale, Calif.) ofa Southern blot of PCR products generated from a Canadian hepatitispatient after hybridization with radiolabeled from Canadian patientGB-C.5.

FIG. 42 depicts a phylogenetic tree produced from alignment of thehelicase domains of the viruses indicated.

FIG. 43 SCOTT depicts a phylogenetic tree produced from alignment of theRNA-dependent RNA polymerase domains of the viruses indicated.

FIG. 44 presents a phylogenetic tree produced from alignment of thelarge open reading frames (putative precursor polyproteins) of theviruses indicated.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides characterization of a newly ascertainedetiological agents of non-A, non-B, non-C, non-D and non-Ehepatitis-causing agents, collectively so-termed “Hepatitis GB Virus,”or “HGBV.” The present invention provides a method for determining thepresence of the HGBV etiological agents, methods for obtaining thenucleic acid of this etiological agents created from infected serum,plasma or liver homogenates from individuals, either humans or tamarins,with HGBV to detect newly synthesized antigens derived from the genomeof heretofore unisolated viral agents, and of selecting clones whichproduced products which are only found in infectious individuals ascompared to non-infected individuals.

Portions of the nucleic acid sequences derived from HGBV are useful asprobes to determine the presence of HGBV in test samples, and to isolatenaturally occurring variants. These sequences also make availablepolypeptide sequences of HGBV antigens encoded within the HGBV genome(s)and permit the production of polypeptides which are useful as standardsor reagents in diagnostic tests and/or as components of vaccines.Monoclonal and polyclonal antibodies directed against at least oneepitope contained within these polypeptide sequences also are useful fordiagnostic tests as well as therapeutic agents, for screening ofantiviral agents, and for the isolation of the HGBV agent from whichthese nucleic acid sequences are derived. Isolation and sequencing ofother portions of the HGBV genome also can be accomplished by utilizingprobes or PCR primers derived from these nucleic acid sequences, thusallowing additional probes and polypeptides of the HGBV to beestablished, which will be useful in the diagnosis and/or treatment ofHGBV, both as a prophylactic and therapeutic agent.

According to one aspect of the invention, there will be provided apurified HGBV polynucleotide, a recombinant HGBV polynucleotide, arecombinant polynucleotide comprising a sequence derived from an HGBVgenome; a recombinant polypeptide encoding an epitope of HGBV; asynthetic peptide encoding an epitope of HGBV; a recombinant vectorcontaining any of the above described recombinant polypeptides, and ahost cell transformed with any of these vectors. These recombinantpolypeptides and synthetic peptides may be used alone or in combination,or in conjunction with other substances representing epitopes of HGBV.

In another aspect of the invention there will be provided purified HGBV;a preparation of polypeptides from the purified HGBV; a purified HGBVpolypeptide; a purified polypeptide comprising an epitope which isimmunologically identical with an epitope contained in HGBV.

In yet another aspect of the invention there will be provided arecombinant expression system comprising an open reading frame (ORF) ofDNA derived from an HGBV genome or from HGBV cDNA, wherein the ORF isoperably linked to a control sequence compatible with a desired host, acell transformed with the recombinant expression system, and apolypeptide produced by the transformed cell.

Additional aspects of the present invention include at least onerecombinant HGBV polypeptide, at least one recombinant polypeptidecomprised of a sequence derived from an HGBV genome or from HGBV cDNA;at least one recombinant polypeptide comprised of an HGBV epitope and atleast one fusion polypeptide comprised of an HGBV polypeptide.

The present invention also provides methods for producing a monoclonalantibody which specifically binds to at least one epitope of HGBV; apurified preparation of polyclonal antibodies which specifically bind toat least one HGBV epitope; and methods for using these antibodies, whichinclude diagnostic, prognostic and therapeutic uses.

In still another aspect of the invention there will be provided aparticle which immunizes against HGBV infection comprising a non-HGBVpolypeptide having an amino acid sequence capable of forming a particlewhen said sequence is produced in an eukaryotic host, and an HGBVepitope.

A polynucleotide probe for HGBV also will be provided.

The present invention provides kits containing reagents which can beused for the detection of the presence and/or amount of polynucleotidesderived from HGBV, such reagents comprising a polynucleotide probecontaining a nucleotide sequence from HGBV of about 8 or morenucleotides in a suitable container; a reagent for detecting thepresence and/or amount of an HGBV antigen comprising an antibodydirected against the HGBV antigen to be detected in a suitablecontainer; a reagent for detecting the presence and/or amount ofantibodies directed against an HGBV antigen comprising a polypeptidecontaining an HGBV epitope present in the HGBV antigen, provided in asuitable container. Other kits for various assay formats also areprovided by the present invention as described herein.

Other aspects of the present invention include a polypeptide comprisingat least one HGBV epitope attached to a solid phase and an antibody toan HGBV epitope attached to a solid phase. Also included are methods forproducing a polypeptide containing an HGBV epitope comprising incubatinghost cells transformed with an expression vector containing a sequenceencoding a polypeptide containing an HGBV epitope under conditions whichallow expression of the polypeptide, and a polypeptide containing anHGBV epitope produced by this method.

The present invention also provides assays which utilize the recombinantor synthetic polypeptides provided by the invention, as well as theantibodies described herein in various formats, any of which may employa signal generating compound in the assay. Assays which do not utilizesignal generating compounds to provide a means of detection also areprovided. All of the assays described generally detect either antigen orantibody, or both, and include contacting a test sample with at leastone reagent provided herein to form at least one antigen/antibodycomplex and detecting the presence of the complex. These assays aredescribed in detail herein.

Vaccines for treatment of HGBV infection comprising an immunogenicpeptide containing an HGBV epitope, or an inactivated preparation ofHGBV, or an attenuated preparation of HGBV, or the use of recombinantvaccines that express HGBV epitope(s) and/or the use of syntheticpeptides, also are included in the present invention. An effectivevaccine may make use of combinations of these immunogenic peptides (suchas, a cocktail of recombinant antigens, synthetic peptides and nativeviral antigens administered simultaneously or at different times); someof these may be utilized alone and be supplemented with otherrepresentations of immunogenic epitopes at later times. Also included inthe present invention is a method for producing antibodies to HGBVcomprising administering to an individual an isolated immunogenicpolypeptide containing an HGBV epitope in an amount sufficient toproduce an immune response in the inoculated individual.

Also provided by the present invention is a tissue culture grown cellinfected with HGBV.

In yet another aspect of the present invention is provided a method forisolating DNA or cDNA derived from the genome of an unidentifiedinfectious agent, which is a unique modification of representationaldifference analysis (RDA), and which is described in detail hereinbelow.

Definitions

The term “Hepatitis GB Virus” or “HGBV”, as used herein, collectivelydenotes a viral species which causes non-A, non-B, non-C, non-D, non-Ehepatitis in man, and attenuated strains or defective interferingparticles derived therefrom. This may include acute viral hepatitistransmitted by contaminated foodstuffs, drinking water, and the like;hepatitis due to HGBV transmitted via person to person contact(including sexual transmission, respiratory and parenteral routes) orvia intravenous drug use. The methods as described herein will allow theidentification of individuals who have acquired HGBV. Individually, theHGBV isolates are specifically referred to as “HGBV-A”, “HGBV-B” and“HGBV-C.” As described herein, the HGBV genome is comprised of RNA.Analysis of the nucleotide sequence and deduced amino acid sequence ofthe HGBV reveals that viruses of this group have a genome organizationsimilar to that of the Flaviridae family. Based primarily, but notexclusively, upon similarities in genome organization, the InternationalCommittee on the Taxonomy of Viruses has recommended that this family becomposed of three genera: Flavivirus, Pestivirus, and the hepatitis Cgroup. Similarity searches at the amino acid level reveal that thehepatitis GB virus subclones have some, albeit low, sequence resemblanceto hepatitis C virus. The information provided herein is sufficient toallow classification of other strains of HGBV.

Several lines of evidence demonstrate that HGBV-C is not a genotype ofHCV. First, sera containing HGB-C sequences were tested for the presenceof HCV antibody. Routine detection of individuals exposed to or infectedwith HCV relies upon antibody tests which utilize antigens derived fromthree or more regions from HCV-1. These tests allow detection ofantibodies to the known genotypes of HCV (See, for example, Sakamoto etal., J. Gen. Virol. 75:1761-1768 (1994) and Stuyver et al., J. Gen.Virol. 74:1093-1102 (1993). HCV-specific ELISAs failed to detect seracontaining GB-C sequences in six of eight cases (TABLE A). Second,several human sera that were seronegative for HCV antibodies have beenshown to be positive for HCV genomic RNA by a highly sensitive RT-PCRassay (Sugitani, Lancet 339:1018-1019 (1992). This assay failed todetect HCV RNA in seven of eight sera containing HGB-C sequences (TABLEA). Thus, HGBV-C is not a genotype of HCV based on both serologic andmolecular assays.

The alignment of a portion of the predicted translation product of HGB-Cwithin the helicase region with the homologous region of HGBV-A, HGBV-B,HCV-1 and additional members of the Flaviviridae, followed byphylogenetic analysis of the aligned sequences suggests that HGBV-C ismore closely related to HGBV-A than to any member of the HCV group. Thesequences of HGBV-C and HGBV-A, while exhibiting an evolutionarydistance of 0.42, are not as divergent as HGBV-C is from HGBV-B, whichshows an evolutionary distance of 0.92 (TABLE 33, infra.). Thus, HGBV-Aand HGBV-C may be considered to be members of one subgroup of the GBviruses and GBV-B a member of its own subgroup. The phylogeneticanalysis of the helicase sequences from various HCV isolates show thatthey form a much less diverged group, exhibiting a maximum evolutionarydistance of 0.20 (TABLE 32, infra.). A comparison of the HCV group andthe HGBV group shows a minimum evolutionary distance between any twosequences from each group of 0.69. The distance values reportedhereinabove were used to generate a phylogenic tree presented in FIG.42. The relatively high degree of divergence among these virusessuggests that the GB viruses are not merely types or subtypes within thehepatitis C group; rather, they constitute their own phyletic group (orgroups). Phylogenetic analysis using sequence information derived from asmall portion of HCV viral genomes has been shown to be an acceptablemethod for the assignment of new isolates into genotypic groups(Simmonds et al., Hepatology 19:1321-1324 (1994). In the currentanalysis, the use of a 110 amino acid sequence within the helicase genefrom representative HCV isolates has properly grouped them into theirrespective genotypes (Simmonds et al., J. Gen. Virol. 75:1053-1061(1994). Therefore, the evolutionary distances shown, in all likelihood,accurately reflect the high degree of divergence between the GB virusesand the hepatitis C virus.

In previous applications, it was stated that “HGBV strains areidentifiable on the polypeptide level and that HGBV strains are morethan 40% homologous, preferably more than about 60% homologous, and evenmore preferably more than about 80% homologous at the polypeptidelevel.” As it is used, the term “homologous,” when referring to thedegree of relatedness of two polynucleotide or polypeptide sequences,can be ambiguous and actually implies an evolutionary relationship. Asis now the current convention in the art, the term “homologous” is nolonger used; instead the terms “similarity” and/or “identity” are usedto describe the degree of relatedness between two polynucleotides orpolypeptide sequences. The techniques for determining amino acidsequence “similarity” and/or “identity” are well-known in the art andinclude, for example, directly determining the amino acid sequence andcomparing it to the sequences provided herein; determining thenucleotide sequence of the genomic material of the putative HGBV(usually via a cDNA intermediate), and determining the amino acidsequence encoded therein, and comparing the corresponding regions. Ingeneral, by “identity” is meant the exact match-up of either thenucleotide sequence of HGBV and that of another strain(s) or the aminoacid sequence of HGBV and that of another strain(s) at the appropriateplace on each genome. Also, in general, by “similarity” is meant theexact match-up of amino acid sequence of HGBV and that of anotherstrain(s) at the appropriate place, where the amino acids are identicalor possess similar chemical and/or physical properties such as charge orhydrophobicity. The programs available in the Wisconsin SequenceAnalysis Package, Version 8 (available from the Genetics Computer Group,Madison, Wis., 53711), for example, the GAP program, are capable ofcalculating both the identity and similarity between two polynucleotideor two polypeptide sequences. Other programs for calculating identityand similarity between two sequences are known in the art.

Additionally, the following parameters are applicable, either alone orin combination, in identifying a strain of HGBV-A, HGBV-B or HGBV-C. Itis expected that the overall nucleotide sequence identity of the genomesbetween HGBV-A, HGBV-B or HGBV-C and a strain of one of these hepatitisGB viruses will be about 45% or greater, since it is now believed thatthe HGBV strains may be genetically related, preferably about 60% orgreater, and more preferably, about 80% or greater.

Also, it is expected that the overall sequence identity of the genomesbetween HGBV-A and a strain of HGBV-A at the amino acid level will beabout 35% or greater since it is now believed that the HGBV strains maybe genetically related, preferably about 40% or greater, morepreferably, about 60% or greater, and even more preferably, about 80% orgreater. In addition, there will be corresponding contiguous sequencesof at least about 13 nucleotides, which may be provided in combinationof more than one contiguous sequence. Also, it is expected that theoverall sequence identity of the genomes between HGBV-B and a strain ofHGBV-B at the amino acid level will be about 35% or greater since it isnow believed that the HGBV strains may be genetically related,preferably about 40% or greater, more preferably, about 60% or greater,and even more preferably, about 80% or greater. In addition, there willbe corresponding contiguous sequences of at least about 13 nucleotides,which may be provided in combination of more than one contiguoussequence. Also, it is expected that the overall sequence identity of thegenomes between HGBV-C and a strain of HGBV-C at the amino acid levelwill be about 35% or greater since it is now believed that the HGBVstrains may be genetically related, preferably about 40% or greater,more preferably, about 60% or greater, and even more preferably, about80% or greater. In addition, there will be corresponding contiguoussequences of at least about 13 nucleotides, which may be provided incombination of more than one contiguous sequence.

The compositions and methods described herein will enable thepropagation, identification, detection and isolation of HGBV and itspossible strains. Moreover, they also will allow the preparation ofdiagnostics and vaccines for the possible different strains of HGBV, andwill have utility in screening procedures for anti-viral agents. Theinformation will be sufficient to allow a viral taxonomist to identifyother strains which fall within the species. We believe that HGBVencodes the sequences that are included herein. Methods for assaying forthe presence of these sequences are known in the art and include, forexample, amplification methods such as ligase chain reaction (LCR),polymerase chain reaction (PCR) and hybridization. In addition, thesesequences contain open reading frames from which an immunogenic viralepitope may be found. This epitope is unique to HGBV when compared toother known hepatitis-causing viruses. The uniqueness of the epitope maybe determined by its immunological reactivity with HGBV and lack ofimmunological reactivity with Hepatitis A, B, C, D and E viruses.Methods for determining immunological reactivity are known in the artand include, for example, radioimmunoassay (RIA), enzyme-linkedimmunosorbant assay (ELISA), hemagglutination (HA), fluorescencepolarization immunoassay (FPIA) and several examples of suitabletechniques are described herein.

A polynucleotide “derived from” a designated sequence for example, theHGBV cDNA, or from the HGBV genome, refers to a polynucleotide sequencewhich is comprised of a sequence of approximately at least about 6nucleotides, is preferably at least about 8 nucleotides, is morepreferably at least about 10-12 nucleotides, and even more preferably isat least about 15-20 nucleotides corresponding, i.e., similar to orcomplementary to, a region of the designated nucleotide sequence.Preferably, the sequence of the region from which the polynucleotide isderived is similar to or complementary to a sequence which is unique tothe HGBV genome. Whether or not a sequence is complementary to orsimilar to a sequence which is unique to an HGBV genome can bedetermined by techniques known to those skilled in the art. Comparisonsto sequences in databanks, for example, can be used as a method todetermine the uniqueness of a designated sequence. Regions from whichsequences may be derived include but are not limited to regions encodingspecific epitopes, as well as non-translated and/or non-transcribedregions.

The derived polynucleotide will not necessarily be derived physicallyfrom the nucleotide sequence of HGBV, but may be generated in anymanner, including but not limited to chemical synthesis, replication orreverse transcription or transcription, which are based on theinformation provided by the sequence of bases in the region(s) fromwhich the polynucleotide is derived. In addition, combinations ofregions corresponding to that of the designated sequence may be modifiedin ways known in the art to be consistent with an intended use.

A “polypeptide” or “amino acid sequence derived from a designatednucleic acid sequence or from the HGBV genome refers to a polypeptidehaving an amino acid sequence identical to that of a polypeptide encodedin the sequence or a portion thereof wherein the portion consists of atleast 3 to 5 amino acids, and more preferably at least 8 to 10 aminoacids, and even more preferably 15 to 20 amino acids, or which isimmunologically identifiable with a polypeptide encoded in the sequence.

A “recombinant polypeptide” as used herein means at least a polypeptideof genomic, semisynthetic or synthetic origin which by virtue of itsorigin or manipulation is not associated with all or a portion of thepolypeptide with which it is associated in nature or in the form of alibrary and/or is linked to a polynucleotide other than that to which itis linked in nature. A recombinant or derived polypeptide is notnecessarily translated from a designated nucleic acid sequence of HGBVor from an HGBV genome. It also may be generated in any manner,including chemical synthesis or expression of a recombinant expressionsystem, or isolation from mutated HGBV.

The term “synthetic peptide” as used herein means a polymeric form ofamino acids of any length, which may be chemically synthesized bymethods well-known to the routineer. These synthetic peptides are usefulin various applications.

The term “polynucleotide” as used herein means a polymeric form ofnucleotides of any length, either ribonucleotides ordeoxyribonucleotides. This term refers only to the primary structure ofthe molecule. Thus, the term includes double- and single-stranded DNA,as well as double- and single-stranded RNA. It also includesmodifications, either by methylation and/or by capping, and unmodifiedforms of the polynucleotide.

“HGBV containing a sequence corresponding to a cDNA” means that the HGBVcontains a polynucleotide sequence which is similar to or complementaryto a sequence in the designated DNA. The degree of similarity orcomplementarity to the cDNA will be approximately 50% or greater, willpreferably be at least about 70%, and even more preferably will be atleast about 90%. The sequence which corresponds will be at least about70 nucleotides, preferably at least about 80 nucleotides, and even morepreferably at least about 90 nucleotides in length. The correspondencebetween the HGBV and the cDNA can be determined by methods known in theart, and include, for example, a direct comparison of the sequencedmaterial with the cDNAs described, or hybridization and digestion withsingle strand nucleases, followed by size determination of the digestedfragments.

“Purified viral polynucleotide” refers to an HGBV genome or fragmentthereof which is essentially free, i.e., contains less than about 50%,preferably less than about 70%, and even more preferably, less thanabout 90% of polypeptides with which the viral polynucleotide isnaturally associated. Techniques for purifying viral polynucleotides arewell known in the art and include, for example, disruption of theparticle with a chaotropic agent, and separation of thepolynucleotide(s) and polypeptides by ion-exchange chromatography,affinity chromatography, and sedimentation according to density. Thus,“purified viral polypeptide” means an HGBV polypeptide or fragmentthereof which is essentially free, that is, contains less than about50%, preferably less than about 70%, and even more preferably, less thanabout 90% of cellular components with which the viral polypeptide isnaturally associated. Methods for purifying are known to the routineer.

“Polypeptide” as used herein indicates a molecular chain of amino acidsand does not refer to a specific length of the product. Thus, peptides,oligopeptides, and proteins are included within the definition ofpolypeptide. This term, however, is not intended to refer topost-expression modifications of the polypeptide, for example,glycosylations, acetylations, phosphorylations and the like.

“Recombinant host cells,” “host cells,” “cells,” “cell lines,” “cellcultures,” and other such terms denoting microorganisms or highereucaryotic cell lines cultured as unicellular entities refer to cellswhich can be, or have been, used as recipients for recombinant vector orother transfer DNA, and include the original progeny of the originalcell which has been transfected.

As used herein “replicon” means any genetic element, such as a plasmid,a chromosome or a virus, that behaves as an autonomous unit ofpolynucleotide replication within a cell. That is, it is capable ofreplication under its own control.

A “vector” is a replicon in which another polynucleotide segment isattached, such as to bring about the replication and/or expression ofthe attached segment.

The term “control sequence refers to polynucleotide sequences which arenecessary to effect the expression of coding sequences to which they areligated. The nature of such control sequences differs depending upon thehost organism. In prokaryotes, such control sequences generally includepromoter, ribosomal binding site and terminators; in eukaryotes, suchcontrol sequences generally include promoters, terminators and, in someinstances, enhancers. The term “control sequence thus is intended toinclude at a minimum all components whose presence is necessary forexpression, and also may include additional components whose presence isadvantageous, for example, leader sequences.

“Operably linked” refers to a situation wherein the components describedare in a relationship permitting them to function in their intendedmanner. Thus, for example, a control sequence “operably-linked” to acoding sequence is ligated in such a manner that expression of thecoding sequence is achieved under conditions compatible with the controlsequences.

The term “open reading frame” or “ORF” refers to a region of apolynucleotide sequence which encodes a polypeptide; this region mayrepresent a portion of a coding sequence or a total coding sequence.

A “coding sequence” is a polynucleotide sequence which is transcribedinto mRNA and/or translated into a polypeptide when placed under thecontrol of appropriate regulatory sequences. The boundaries of thecoding sequence are determined by a translation start codon at the5′-terminus and a translation stop codon at the 3′-terminus. A codingsequence can include, but is not limited to, mRNA, cDNA, and recombinantpolynucleotide sequences.

The term “immunologically identifiable with/as” refers to the presenceof epitope(s) and polypeptide(s) which also are present in and areunique to the designated polypeptide(s), usually HGBV proteins.Immunological identity may be determined by antibody binding and/orcompetition in binding. These techniques are known to the routineer andalso are described herein. The uniqueness of an epitope also can bedetermined by computer searches of known data banks, such as GenBank,for the polynucleotide sequences which encode the epitope, and by aminoacid sequence comparisons with other known proteins.

As used herein, “epitope” means an antigenic determinant of apolypeptide. Conceivably, an epitope can comprise three amino acids in aspatial conformation which is unique to the epitope. Generally, anepitope consists of at least five such amino acids, and more usually, itconsists of at least eight to ten amino acids. Methods of examiningspatial conformation are known in the art and include, for example,x-ray crystallography and two-dimensional nuclear magnetic resonance.

A polypeptide is “immunologically reactive” with an antibody when itbinds to an antibody due to antibody recognition of a specific epitopecontained within the polypeptide. Immunological reactivity may bedetermined by antibody binding, more particularly by the kinetics ofantibody binding, and/or by competition in binding using ascompetitor(s) a known polypeptide(s) containing an epitope against whichthe antibody is directed. The methods for determining whether apolypeptide is immunologically reactive with an antibody are known inthe art.

As used herein, the term “immunogenic polypeptide containing an HGBVepitope” means naturally occurring HGBV polypeptides or fragmentsthereof, as well as polypeptides prepared by other means, for example,chemical synthesis or the expression of the polypeptide in a recombinantorganism.

The term “transformation” refers to the insertion of an exogenouspolynucleotide into a host cell, irrespective of the method used for theinsertion. For example, direct uptake, transduction, or f-mating areincluded. The exogenous polynucleotide may be maintained as anon-integrated vector, for example, a plasmid, or alternatively, may beintegrated into the host genome.

“Treatment” refers to prophylaxis and/or therapy.

The term “individual” as used herein refers to vertebrates, particularlymembers of the mammalian species and includes but is not limited todomestic animals, sports animals, primates and humans; more particularlythe term refers to tamarins and humans.

The term “plus strand” (or “+”) as used herein denotes a nucleic acidthat contains the sequence that encodes the polypeptide. The term “minusstrand” (or “−”) denotes a nucleic acid that contains a sequence that iscomplementary to that of the “plus” strand.

“Positive stranded genome” of a virus denotes that the genome, whetherRNA or DNA, is single-stranded and which encodes a viral polypeptide(s).

The term “test sample” refers to a component of an individual's bodywhich is the source of the analyte (such as, antibodies of interest orantigens of interest). These components are well known in the art. Thesetest samples include biological samples which can be tested by themethods of the present invention described herein and include human andanimal body fluids such as whole blood, serum, plasma, cerebrospinalfluid, urine, lymph fluids, and various external secretions of therespiratory, intestinal and genitourinary tracts, tears, saliva, milk,white blood cells, myelomas and the like; biological fluids such as cellculture supernatants; fixed tissue specimens; and fixed cell specimens.

“Purified HGBV” refers to a preparation of HGBV which has been isolatedfrom the cellular constituents with which the virus is normallyassociated, and from other types of viruses which may be present in theinfected tissue. The techniques for isolating viruses are known to thoseskilled in the art and include, for example, centrifugation and affinitychromatography.

“PNA” denotes a “peptide nucleic analog” which may be utilized in aprocedure such as an assay to determine the presence of a target. PNAsare neutrally charged moieties which can be directed against RNA targetsor DNA. PNA probes used in assays in place of, for example, DNA probes,offer advantages not achievable when DNA probes are used. Theseadvantages include manufacturability, large scale labeling,reproducibility, stability, insensitivity to changes in ionic strengthand resistance to enzymatic degradation which is present in methodsutilizing DNA or RNA. These PNAs can be labeled with such signalgenerating compounds as fluorescein, radionucleotides, chemiluminescentcompounds, and the like. PNAs thus can be used in methods in place ofDNA or RNA. Although assays are described herein utilizing DNA, it iswithin the scope of the routineer that PNAs can be substituted for RNAor DNA with appropriate changes if and as needed in assay reagents.

General Uses

After preparing recombinant proteins, synthetic peptides, or purifiedviral polypeptides of choice as described by the present invention, therecombinant or synthetic peptides can be used to develop unique assaysas described herein to detect either the presence of antigen or antibodyto HGBV. These compositions also can be used to develop monoclonaland/or polyclonal antibodies with a specific recombinant protein orsynthetic peptide which specifically bind to the immunological epitopeof HGBV which is desired by the routineer. Also, it is contemplated thatat least one polynucleotide of the invention can be used to developvaccines by following methods known in the art.

It is contemplated that the reagent employed for the assay can beprovided in the form of a test kit with one or more containers such asvials or bottles, with each container containing a separate reagent suchas a monoclonal antibody, or a cocktail of monoclonal antibodies, or apolypeptide (either recombinant or synthetic) employed in the assay.Other components such as buffers, controls, and the like, known to thoseof ordinary skill in art, may be included in such test kits.

“Solid phases” (“solid supports”) are known to those in the art andinclude the walls of wells of a reaction tray, test tubes, polystyrenebeads, magnetic beads, nitrocellulose strips, membranes, microparticlessuch as latex particles, sheep (or other animal) red blood cells,Duracytes (derivatized red blood cells, available from AbbottLaboratories, Abbott Park, Ill.) and others. The “solid phase” is notcritical and can be selected by one skilled in the art. Thus, latexparticles, microparticles, magnetic or non-magnetic beads, membranes,plastic tubes, walls of microtiter wells, glass or silicon chips, sheep(or other suitable animal's) red blood cells and Duracytes are allsuitable examples. Suitable methods for immobilizing peptides on solidphases include ionic, hydrophobic, covalent interactions and the like. A“solid phase”, as used herein, refers to any material which isinsoluble, or can be made insoluble by a subsequent reaction. The solidphase can be chosen for its intrinsic ability to attract and immobilizethe capture reagent. Alternatively, the solid phase can retain anadditional receptor which has the ability to attract and immobilize thecapture reagent. The additional receptor can include a charged substancethat is oppositely charged with respect to the capture reagent itself orto a charged substance conjugated to the capture reagent. As yet anotheralternative, the receptor molecule can be any specific binding memberwhich is immobilized upon (attached to) the solid phase and which hasthe ability to immobilize the capture reagent through a specific bindingreaction. The receptor molecule enables the indirect binding of thecapture reagent to a solid phase material before the performance of theassay or during the performance of the assay. The solid phase thus canbe a plastic, derivatized plastic, magnetic or non-magnetic metal, glassor silicon surface of a test tube, microtiter well, sheet, bead,microparticle, chip, sheep (or other suitable animal's) red blood cells,Duracytes and other configurations known to those of ordinary skill inthe art.

It is contemplated and within the scope of the invention that the solidphase also can comprise any suitable porous material with sufficientporosity to allow access by detection antibodies and a suitable surfaceaffinity to bind antigens. Microporous structures are generallypreferred, but materials with gel structure in the hydrated state may beused as well. Such useful solid supports include: natural polymericcarbohydrates and their synthetically modified, cross-linked orsubstituted derivatives, such as agar, agarose, cross-linked alginicacid, substituted and cross-linked guar gums, cellulose esters,especially with nitric acid and carboxylic acids, mixed celluloseesters, and cellulose ethers; natural polymers containing nitrogen, suchas proteins and derivatives, including cross-linked or modifiedgelatins; natural hydrocarbon polymers, such as latex and rubber;synthetic polymers which may be prepared with suitably porousstructures, such as vinyl polymers, including polyethylene,polypropylene, polystyrene, polyvinylchloride, polyvinylacetate and itspartially hydrolyzed derivatives, polyacrylamides, polymethacrylates,copolymers and terpolymers of the above polycondensates, such aspolyesters, polyamides, and other polymers, such as polyurethanes orpolyepoxides; porous inorganic materials such as sulfates or carbonatesof alkaline earth metals and magnesium, including barium sulfate,calcium sulfate, calcium carbonate, silicates of alkali and alkalineearth metals, aluminum and magnesium; and aluminum or silicon oxides orhydrates, such as clays, alumina, talc, kaolin, zeolite, silica gel, orglass (these materials may be used as filters with the above polymericmaterials); and mixtures or copolymers of the above classes, such asgraft copolymers obtained by initializing polymerization of syntheticpolymers on a pre-existing natural polymer. All of these materials maybe used in suitable shapes, such as films, sheets, or plates, or theymay be coated onto or bonded or laminated to appropriate inert carriers,such as paper, glass, plastic films, or fabrics.

The porous structure of nitrocellulose has excellent absorption andadsorption qualities for a wide variety of reagents including monoclonalantibodies. Nylon also possesses similar characteristics and also issuitable. It is contemplated that such porous solid supports describedhereinabove are preferably in the form of sheets of thickness from about0.01 to 0.5 mm, preferably about 0.1 mm. The pore size may vary withinwide limits, and is preferably from about 0.025 to 15 microns,especially from about 0.15 to 15 microns. The surfaces of such supportsmay be activated by chemical processes which cause covalent linkage ofthe antigen or antibody to the support. The irreversible binding of theantigen or antibody is obtained, however, in general, by adsorption onthe porous material by poorly understood hydrophobic forces. Suitablesolid supports also are described in U.S. patent application Ser. No.227,272.

The “indicator reagent” comprises a “signal generating compound” (label)which is capable of generating and generates a measurable signaldetectable by external means conjugated (attached) to a specific bindingmember for HGBV. “Specific binding member” as used herein means a memberof a specific binding pair. That is, two different molecules where oneof the molecules through chemical or physical means specifically bindsto the second molecule. In addition to being an antibody member of aspecific binding pair for HGBV, the indicator reagent also can be amember of any specific binding pair, including either hapten-anti-haptensystems such as biotin or anti-biotin, avidin or biotin, a carbohydrateor a lectin, a complementary nucleotide sequence, an effector or areceptor molecule, an enzyme cofactor and an enzyme, an enzyme inhibitoror an enzyme, and the like. An immunoreactive specific binding membercan be an antibody, an antigen, or an antibody/antigen complex that iscapable of binding either to HGBV as in a sandwich assay, to the capturereagent as in a competitive assay, or to the ancillary specific bindingmember as in an indirect assay.

The various “signal generating compounds” (labels) contemplated includechromagens, catalysts such as enzymes, luminescent compounds such asfluorescein and rhodamine, chemiluminescent compounds such asdioxetanes, acridiniums, phenanthridiniums and luminol, radioactiveelements, and direct visual labels. Examples of enzymes include alkalinephosphatase, horseradish peroxidase, beta-galactosidase, and the like.The selection of a particular label is not critical, but it will becapable of producing a signal either by itself or in conjunction withone or more additional substances.

The present invention provides assays which utilize specific bindingmembers. A “specific binding member,” as used herein, is a member of aspecific binding pair. That is, two different molecules where one of themolecules through chemical or physical means specifically binds to thesecond molecule. Therefore, in addition to antigen and antibody specificbinding pairs of common immunoassays, other specific binding pairs caninclude biotin and avidin, carbohydrates and lectins, complementarynucleotide sequences, effector and receptor molecules, cofactors andenzymes, enzyme inhibitors and enzymes, and the like. Furthermore,specific binding pairs can include members that are analogs of theoriginal specific binding members, for example, an analyte-analog.Immunoreactive specific binding members include antigens, antigenfragments, antibodies and antibody fragments, both monoclonal andpolyclonal, and complexes thereof, including those formed by recombinantDNA molecules. The term “hapten”, as used herein, refers to a partialantigen or non-protein binding member which is capable of binding to anantibody, but which is not capable of eliciting antibody formationunless coupled to a carrier protein.

“Analyte,” as used herein, is the substance to be detected which may bepresent in the test sample. The analyte can be any substance for whichthere exists a naturally occurring specific binding member (such as, anantibody), or for which a specific binding member can be prepared. Thus,an analyte is a substance that can bind to one or more specific bindingmembers in an assay. “Analyte” also includes any antigenic substances,haptens, antibodies, and combinations thereof. As a member of a specificbinding pair, the analyte can be detected by means of naturallyoccurring specific binding partners (pairs) such as the use of intrinsicfactor protein as a member of a specific binding pair for thedetermination of Vitamin B12, the use of folate-binding protein todetermine folic acid, or the use of a lectin as a member of a specificbinding pair for the determination of a carbohydrate. The analyte caninclude a protein, a peptide, an amino acid, a nucleotide target, andthe like.

Other embodiments which utilize various other solid phases also arecontemplated and are within the scope of this invention. For example,ion capture procedures for immobilizing an immobilizable reactioncomplex with a negatively charged polymer, described in co-pending U.S.patent application Ser. No. 150,278 corresponding to EP publication0326100 and U.S. patent application Ser. No. 375,029 (EP publication no.0406473), can be employed according to the present invention to effect afast solution-phase immunochemical reaction. An immobilizable immunecomplex is separated from the rest of the reaction mixture by ionicinteractions between the negatively charged poly-anion/immune complexand the previously treated, positively charged porous matrix anddetected by using various signal generating systems previouslydescribed, including those described in chemiluminescent signalmeasurements as described in co-pending U.S. patent application Ser. No.921,979 corresponding to EPO Publication No. 0 273,115.

Also, the methods of the present invention can be adapted for use insystems which utilize microparticle technology including in automatedand semi-automated systems wherein the solid phase comprises amicroparticle (magnetic or non-magnetic). Such systems include thosedescribed in pending U.S. patent applications Ser. Nos. 425,651 and425,643, which correspond to published EPO applications Nos. EP 0 425633 and EP 0 424 634, respectively.

The use of scanning probe microscopy (SPM) for immunoassays also is atechnology to which the monoclonal antibodies of the present inventionare easily adaptable. In scanning probe microscopy, in particular inatomic force microscopy, the capture phase, for example, at least one ofthe monoclonal antibodies of the invention, is adhered to a solid phaseand a scanning probe microscope is utilized to detect antigen/antibodycomplexes which may be present on the surface of the solid phase. Theuse of scanning tunnelling microscopy eliminates the need for labelswhich normally must be utilized in many immunoassay systems to detectantigen/antibody complexes. Such a system is described in pending U.S.patent application Ser. No. 662,147. The use of SPM to monitor specificbinding reactions can occur in many ways. In one embodiment, one memberof a specific binding partner (analyte specific substance which is themonoclonal antibody of the invention) is attached to a surface suitablefor scanning. The attachment of the analyte specific substance may be byadsorption to a test piece which comprises a solid phase of a plastic ormetal surface, following methods known to those of ordinary skill in theart. Or, covalent attachment of a specific binding partner (analytespecific substance) to a test piece which test piece comprises a solidphase of derivatized plastic, metal, silicon, or glass may be utilized.Covalent attachment methods are known to those skilled in the art andinclude a variety of means to irreversibly link specific bindingpartners to the test piece. If the test piece is silicon or glass, thesurface must be activated prior to attaching the specific bindingpartner. Activated silane compounds such as triethoxy amino propylsilane (available from Sigma Chemical Co., St. Louis, Mo.), triethoxyvinyl silane (Aldrich Chemical Co., Milwaukee, Wis.), and(3-mercapto-propyl)-trimethoxy silane (Sigma Chemical Co., St. Louis,Mo.) can be used to introduce reactive groups such as amino-, vinyl, andthiol, respectively. Such activated surfaces can be used to link thebinding partner directly (in the cases of amino or thiol) or theactivated surface can be further reacted with linkers such asglutaraldehyde, bis (succinimidyl) suberate, SPPD 9 succinimidyl3-[2-pyridyldithio]propionate), SMCC(succinimidyl-4-[N-maleimidomethyl]cyclohexane-1-carboxylate), SIAB(succinimidyl[4-iodoacetyl]aminobenzoate), and SMPB (succinimidyl4-[1-maleimidophenyl]butyrate) to separate the binding partner from thesurface. The vinyl group can be oxidized to provide a means for covalentattachment. It also can be used as an anchor for the polymerization ofvarious polymers such as poly acrylic acid, which can provide multipleattachment points for specific binding partners. The amino surface canbe reacted with oxidized dextrans of various molecular weights toprovide hydrophilic linkers of different size and capacity. Examples ofoxidizable dextrans include Dextran T-40 (molecular weight 40,000daltons), Dextran T-110 (molecular weight 110,000 daltons), DextranT-500 (molecular weight 500,000 daltons), Dextran T-2M (molecular weight2,000,000 daltons) (all of which are available from Pharmacia), orFicoll (molecular weight 70,000 daltons (available from Sigma ChemicalCo., St. Louis, Mo.). Also, polyelectrolyte interactions may be used toimmobilize a specific binding partner on a surface of a test piece byusing techniques and chemistries described by pending U.S. Patentapplications Ser. No. 150,278, filed Jan. 29, 1988, and Ser. No.375,029, filed Jul. 7, 1989. The preferred method of attachment is bycovalent means. Following attachment of a specific binding member, thesurface may be further treated with materials such as serum, proteins,or other blocking agents to minimize non-specific binding. The surfacealso may be scanned either at the site of manufacture or point of use toverify its suitability for assay purposes. The scanning process is notanticipated to alter the specific binding properties of the test piece.

Various other assay formats may be used, including “sandwich”immunoassays and probe assays. For example, the monoclonal antibodies ofthe present invention can be employed in various assay systems todetermine the presence, if any, of HGBV proteins in a test sample.Fragments of these monoclonal antibodies provided also may be used. Forexample, in a first assay format, a polyclonal or monoclonal anti-HGBVantibody or fragment thereof, or a combination of these antibodies,which has been coated on a solid phase, is contacted with a test samplewhich may contain HGBV proteins, to form a mixture. This mixture isincubated for a time and under conditions sufficient to formantigen/antibody complexes. Then, an indicator reagent comprising amonoclonal or a polyclonal antibody or a fragment thereof, whichspecifically binds to an HGBV region, or a combination of theseantibodies, to which a signal generating compound has been attached, iscontacted with the antigen/antibody complexes to form a second mixture.This second mixture then is incubated for a time and under conditionssufficient to form antibody/antigen/antibody complexes. The presence ofHGBV antigen present in the test sample and captured on the solid phase,if any, is determined by detecting the measurable signal generated bythe signal generating compound. The amount of HGBV antigen present inthe test sample is proportional to the signal generated.

Alternatively, a polyclonal or monoclonal anti-HGBV antibody or fragmentthereof, or a combination of these antibodies which is bound to a solidsupport, the test sample and an indicator reagent comprising amonoclonal or polyclonal antibody or fragments thereof, whichspecifically binds to HGBV antigen, or a combination of these antibodiesto which a signal generating compound is attached, are contacted to forma mixture. This mixture is incubated for a time and under conditionssufficient to form antibody/antigen/antibody complexes. The presence, ifany, of HGBV proteins present in the test sample and captured on thesolid phase is determined by detecting the measurable signal generatedby the signal generating compound. The amount of HGBV proteins presentin the test sample is proportional to the signal generated.

In another alternate assay format, one or a combination of at least twomonoclonal antibodies of the invention can be employed as a competitiveprobe for the detection of antibodies to HGBV protein. For example, HGBVproteins, either alone or in combination, can be coated on a solidphase. A test sample suspected of containing antibody to HGBV antigenthen is incubated with an indicator reagent comprising a signalgenerating compound and at least one monoclonal antibody of theinvention for a time and under conditions sufficient to formantigen/antibody complexes of either the test sample and indicatorreagent to the solid phase or the indicator reagent to the solid phase.The reduction in binding of the monoclonal antibody to the solid phasecan be quantitatively measured. A measurable reduction in the signalcompared to the signal generated from a confirmed negative NANB, non-C,non-D, non-E hepatitis test sample indicates the presence of anti-HGBVantibody in the test sample.

In yet another detection method, each of the monoclonal or polyclonalantibodies of the present invention can be employed in the detection ofHGBV antigens in fixed tissue sections, as well as fixed cells byimmunohistochemical analysis. Cytochemical analysis wherein theseantibodies are labeled directly (fluorescein, colloidal gold,horseradish peroxidase, alkaline phosphatase, etc.) or are labeled byusing secondary labeled anti-species antibodies (with various labels asexemplified herein) to track the histopathology of disease also arewithin the scope of the present invention.

In addition, these monoclonal antibodies can be bound to matricessimilar to CNBr-activated Sepharose and used for the affinitypurification of specific HGBV proteins from cell cultures, or biologicaltissues such as blood and liver such as to purify recombinant and nativeviral HGBV antigens and proteins.

The monoclonal antibodies of the invention can also be used for thegeneration of chimeric antibodies for therapeutic use, or other similarapplications.

The monoclonal antibodies or fragments thereof can be providedindividually to detect HGBV antigens. Combinations of the monoclonalantibodies (and fragments thereof) provided herein also may be usedtogether as components in a mixture or “cocktail” of at least oneanti-HGBV antibody of the invention with antibodies to other HGBVregions, each having different binding specificities. Thus, thiscocktail can include the monoclonal antibodies of the invention whichare directed to HGBV proteins and other monoclonal antibodies to otherantigenic determinants of the HGBV genome.

The polyclonal antibody or fragment thereof which can be used in theassay formats should specifically bind to a specific HGBV region orother HGBV proteins used in the assay. The polyclonal antibody usedpreferably is of mammalian origin; human, goat, rabbit or sheepanti-HGBV polyclonal antibody can be used. Most preferably, thepolyclonal antibody is rabbit polyclonal anti-HGBV antibody. Thepolyclonal antibodies used in the assays can be used either alone or asa cocktail of polyclonal antibodies. Since the cocktails used in theassay formats are comprised of either monoclonal antibodies orpolyclonal antibodies having different HGBV specificity, they would beuseful for diagnosis, evaluation and prognosis of HGBV infection, aswell as for studying HGBV protein differentiation and specificity.

It is contemplated and within the scope of the present invention thatthe HGBV group of viruses may be detectable in assays by use of asynthetic, recombinant or native peptide that is common to all HGBVviruses. It also is within the scope of the present invention thatdifferent synthetic, recombinant or native peptides identifyingdifferent epitopes from HGBV-A, HGBV-B, HGBV-C, or yet other HGBVviruses, can be used in assay formats. In the later case, these can becoated onto one solid phase, or each separate peptide may be coated onseparate solid phases, such as microparticles, and then combined to forma mixture of peptides which can be later used in assays. Such variationsof assay formats are known to those of ordinary skill in the art and arediscussed hereinbelow.

In another assay format, the presence of antibody and/or antigen to HGBVcan be detected in a simultaneous assay, as follows. A test sample issimultaneously contacted with a capture reagent of a first analyte,wherein said capture reagent comprises a first binding member specificfor a first analyte attached to a solid phase and a capture reagent fora second analyte, wherein said capture reagent comprises a first bindingmember for a second analyte attached to a second solid phase, to therebyform a mixture. This mixture is incubated for a time and underconditions sufficient to form capture reagent/first analyte and capturereagent/second analyte complexes. These so-formed complexes then arecontacted with an indicator reagent comprising a member of a bindingpair specific for the first analyte labeled with a signal generatingcompound and an indicator reagent comprising a member of a binding pairspecific for the second analyte labeled with a signal generatingcompound to form a second mixture. This second mixture is incubated fora time and under conditions sufficient to form capture reagent/firstanalyte/indicator reagent complexes and capture reagent/secondanalyte/indicator reagent complexes. The presence of one or moreanalytes is determined by detecting a signal generated in connectionwith the complexes formed on either or both solid phases as anindication of the presence of one or more analytes in the test sample.In this assay format, proteins derived from human expression systems maybe utilized as well as monoclonal antibodies produced from the proteinsderived from the mammalian expression systems as disclosed herein. Suchassay systems are described in greater detail in pending U.S. patentapplication Ser. No. 07/574,821 entitled Simultaneous Assay forDetecting One Or More Analytes, which corresponds to EP Publication No.0473065.

In yet other assay formats, recombinant proteins and/or syntheticpeptides may be utilized to detect the presence of anti-HGBV in testsamples. For example, a test sample is incubated with a solid phase towhich at least one recombinant protein or synthetic peptide has beenattached. These are reacted for a time and under conditions sufficientto form antigen/antibody complexes. Following incubation, theantigen/antibody complex is detected. Indicator reagents may be used tofacilitate detection, depending upon the assay system chosen. In anotherassay format, a test sample is contacted with a solid phase to which arecombinant protein or synthetic peptide produced as described herein isattached and also is contacted with a monoclonal or polyclonal antibodyspecific for the protein, which preferably has been labeled with anindicator reagent. After incubation for a time and under conditionssufficient for antibody/antigen complexes to form, the solid phase isseparated from the free phase, and the label is detected in either thesolid or free phase as an indication of the presence of HGBV antibody.Other assay formats utilizing the proteins of the present invention arecontemplated. These include contacting a test sample with a solid phaseto which at least one antigen from a first source has been attached,incubating the solid phase and test sample for a time and underconditions sufficient to form antigen/antibody complexes, and thencontacting the solid phase with a labeled antigen, which antigen isderived from a second source different from the first source. Forexample, a recombinant protein derived from a first source such as E.coli is used as a capture antigen on a solid phase, a test sample isadded to the so-prepared solid phase, and a recombinant protein derivedfrom a different source (i.e., non-E. coli) is utilized as a part of anindicator reagent. Likewise, combinations of a recombinant antigen on asolid phase and synthetic peptide in the indicator phase also arepossible. Any assay format which utilizes an antigen specific for HGBVfrom a first source as the capture antigen and an antigen specific forHGBV from a different second source are contemplated. Thus, variouscombinations of recombinant antigens, as well as the use of syntheticpeptides, purified viral proteins, and the like, are within the scope ofthis invention. Assays such as this and others are described in U.S.Pat. No. 5,254,458, which enjoys common ownership and is incorporatedherein by reference.

Other assay systems which utilize an antibody (polyclonal, monoclonal ornaturally-occurring) which specifically binds HGBV viral particles orsub-viral particles housing the viral genome (or fragments thereof) byvirtue of a contact between the specific antibody and the viral protein(peptide, etc.). This captured particle then can be analyzed by methodssuch as LCR or PCR to determine whether the viral genome is present inthe test sample. Test samples which can be assayed according to thismethod include blood, liver, sputum, urine, fecal material, saliva, andthe like. The advantage of utilizing such an antigen captureamplification method is that it can separate the viral genome from othermolecules in the test specimen by use of a specific antibody. Such amethod has been described in pending U.S. patent application Ser. No.08/141,429.

While the present invention discloses the preference for the use ofsolid phases, it is contemplated that the reagents such as antibodies,proteins and peptides of the present invention can be utilized innon-solid phase assay systems. These assay systems are known to thoseskilled in the art, and are considered to be within the scope of thepresent invention.

Materials and Methods

General Techniques

Conventional and well-known techniques and methods in the fields ofmolecular biology, microbiology, recombinant DNA and immunology areemployed in the practice of the invention unless otherwise noted. Suchtechniques are explained and detailed in the literature. See, forexample, J. Sambrook et al., Molecular Cloning: A Laboratory Manual, 2ndedition, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989); D.N. Glover, ed., DNA Cloning, Volumes I and II (1985); M. J. Gait ed.,Oligonucleotide Synthesis, (1984); B. D. Hames et al., eds., NucleicAcid Hybridization, (1984); B. D. Hames et al., eds., Transcription andTranslation, (1984); R. I. Freshney ed., Animal Cell Culture, (1986);Immobilized Cells and Enzymes, IRL Press (1986); B. Perbal, A PracticalGuide to Molecular Cloning, (1984); the series, Methods in Enzymology,Academic Press, Inc., Orlando, Fla.; J. H. Miller et al., eds., GeneTransfer Vectors For Mammalian Cells, Cold Spring Harbor Laboratory,Cold Spring Harbor, N.Y. (1987); Wu et al., eds., Methods in Enzymology,Vol. 154 and 155; Mayer et al., eds., Immunological Methods In Cell andMolecular Biology, Academic Press, London (1987); Scopes, ProteinPurification: Principles and Practice, 2nd ed., Springer-Verlag, N.Y.;and D. Weir et al., eds., Handbook Of Experimental Immunology, VolumesI-IV (1986); N. Lisitisyn et al., Science 259:946-951 (1993).

The reagents and methods of the present invention are made possible bythe provision of a family of closely related nucleotide sequences,isolated by representational difference analysis modified as describedherein, present in the plasma, serum or liver homogenate of an HGBVinfected individual, either tamarin or human. This family of nucleotidesequences is not of human or tamarin origin, since it will be shown thatit hybridizes to neither human nor tamarin genomic DNA from uninfectedindividuals, since nucleotides of this family of sequences are presentonly in liver (or liver homogenates), plasma or serum of individualsinfected with HGBV, and since the sequence is not present in GenBank. Inaddition, the family of sequences will show no significant identity atthe nucleic acid level to sequences contained within the HAV, HBV, HCV,HDV and HEV genome, and low level identity, considered not significant,as translation products. Infectious sera, plasma or liver homogenatesfrom HGBV infected humans contain these polynucleotide sequences,whereas sera, plasma or liver homogenates from non-infected humans donot contain these sequences. Northern blot analysis of infected liverwith some of these polynucleotide sequences demonstrate that they arederived from a large RNA transcript similar in size to a viral genome.Sera, plasma or liver homogenates from HGBV-infected humans containantibodies which bind to this polypeptide, whereas sera, plasma or liverhomogenates from non-infected humans do not contain antibodies to thispolypeptide; these antibodies are induced in individuals following acutenon-A, non-B, non-C, non-D and non-E infection. By these criteria, it isbelieved that the sequence is a viral sequence, wherein the virus causesor is associated with non-A, non-B, non-C, non-D and non-E hepatitis.

The availability of this family of nucleic acid sequences permits theconstruction of DNA probes and polypeptides useful in diagnosing non-A,non-B, non-C, non-D, non-E hepatitis due to HGBV infections, and inscreening blood donors, donated blood, blood products and individualsfor infection. For example, from the sequence it is possible tosynthesize DNA oligomers of about eight to ten nucleotides, or larger,which are useful as hybridization probes or PCR primers to detect thepresence of the viral genome in, for example, sera of subjects suspectedof harboring the virus, or for screening donated blood for the presenceof the virus. The family of nucleic acid sequences also allows thedesign and production of HGBV specific polypeptides which are useful asdiagnostic reagents for the presence of antibodies raised duringinfection with HGBV. Antibodies to purified polypeptides derived fromthe nucleic acid sequences may also be used to detect viral antigens ininfected individuals and in blood. These nucleic acid sequences alsoenable the design and production of polypeptides which may be used asvaccines against HGBV, and also for the production of antibodies, whichthen may be used for protection of the disease, and/or for therapy ofHGBV infected individuals.

The family of nucleic acid sequences also enables furthercharacterization of the HGBV genome. Polynucleotide probes derived fromthese sequences may be used to screen genomic or cDNA libraries foradditional overlapping nucleic acid sequences which then may be used toobtain more overlapping sequences. Unless the genome is segmented andthe segments lack common sequences, this technique may be used to gainthe sequence of the entire genome. However, if the genome is segmented,other segments of the genome can be obtained by either repeating the RDAcloning procedure as described and modified hereinbelow or by repeatingthe lambda-gt11 serological screening procedure discussed hereinbelow toisolate the clones which will be described herein, or alternatively byisolating the genome from purified HGBV particles.

The family of cDNA sequences and the polypeptides derived from thesesequences, as well as antibodies directed against these polypeptides,also are useful in the isolation and identification of the HGBVetiological agent(s). For example, antibodies directed against HGBVepitopes contained in polypeptides derived from the nucleic acidsequences may be used in methods based upon affinity chromatography toisolate the virus. Alternatively, the antibodies can be used to identifyviral particles isolated by other techniques. The viral antigens and thegenomic material within the isolated viral particles then may be furthercharacterized.

The information obtained from further sequencing of the HGBV genome(s),as well as from further characterization of the HGBV antigens andcharacterization of the genome enables the design and synthesis ofadditional probes and polypeptides and antibodies which may be used fordiagnosis, prevention and therapy of HGBV induced non-A, non-B, non-Cnon-D, non-E hepatitis, and for screening of infected blood andblood-related products.

The availability of probes for HGBV, including antigens, antibodies andpolynucleotides derived from the genome from which the family of nucleicacid sequences is derived also allows for the development of tissueculture systems which will be of major use in elucidating the biology ofHGBV. Once this is known, it is contemplated that new treatment regimensmay be developed based upon antiviral compounds which preferentiallyinhibit the replication of or infection by HGBV.

In one method used to identify and isolate the etiological agent ofHGBV, the cloning/isolation of the GB agent was achieved by modifyingthe published procedure known as representational difference analysis(RDA), as reported by N. Lisitsyn et al., Science 259: 946-951 (1993).This method is based upon the principles of subtractive hybridizationfor cloning DNA differences between two complex mammalian genomes.Briefly, in this procedure, the two genomes under evaluation areidentified generically as the “tester” (containing the target sequenceof interest) and the “driver” (representing normal DNA). Lisitsyn etal.'s description of RDA is limited to identifying and cloning DNAdifferences between complex, but similar DNA backgrounds. Thesedifferences may include any large DNA viruses (eg. ≧5,000 base pairs ofDNA) that is present in a cell line, blood, plasma or tissue sample andabsent in an uninfected cell line, blood, plasma or tissue sample.Because previous literature suggested that HGBV may be a small viruscontaining either a DNA or RNA genome of ≦10,000 bases, the RDA protocolwas modified such as to allow the detection of small viruses. The majorsteps of the procedure are described hereinbelow and are diagrammed inFIG. 13.

Briefly, in step 1, total nucleic acid (DNA and RNA) is isolated usingcommercially available kits. RDA requires that the sample be highlymatched. Ideally, tester and driver nucleic acid samples should beobtained from the same source (animal, human or other). It may bepossible to use highly related, but non-identical, material for thesource of the tester and driver nucleic acids. Double stranded DNA isgenerated from the total nucleic acid by random primed reversetranscription of the RNA followed by random primed DNA synthesis. Thistreatment converts single strand RNA viruses and single strand DNAviruses to double strand DNA molecules which are amenable to RDA. If onechooses to assume that an unknown virus has a DNA or an RNA genome, aDNA-only or RNA-only extraction procedure can be employed anddouble-stranded DNA can be generated as described in the art.

In step 2, the tester and driver nucleic acids are amplified to generatean abundant amount of material which represents the total nucleic acidextracted from the pre-inoculation and infectious plasma sources (i.e.the tester amplicon and the driver amplicon). This is achieved bycleaving double-stranded DNA prepared as described above with arestriction endonuclease which has a 4 bp recognition site (such asSau3A I). The DNA fragments are ligated to oligonucleotide adaptors (set#1). The DNA fragments are end-filled and PCR amplified. Following PCRamplification, the oligonucleotide adaptor (set #1) is then removed byrestriction endonuclease digestion (for example, with Sau3A I),liberating a large amount of tester and driver nucleic acid to be usedin subsequent subtractive hybridization techniques.

In step 3, the experimental design is to enrich for DNA unique to thetester genome. This is achieved by combining subtractive hybridizationand kinetic enrichment into a single step. Briefly, an oligonucleotideadaptor set (#2 or #3) is ligated to the 5′ ends of the tester amplicon.The tester amplicon and an excess of driver amplicon are mixed,denatured and allowed to hybridized for 20 hours. A large amount of thesequences that are held in common between the tester and driver DNA willanneal during this time. In addition, sequences that are unique to thetester amplicon will reanneal. However, because of the limited time ofhybridization, some single-stranded tester and driver DNA will remain.

In step 4, the 3′ ends of the reannealed tester and driver DNA arefilled in using a thermostable DNA polymerase at elevated temperature asdescribed in the art. The reannealed sequences that are unique to thetester contain the ligated adaptor on both strands of the annealedsequence. Thus, 3′ end-filling of these molecules creates sequencescomplementary to PCR primers on both DNA strands. As such, these DNAspecies will be amplified exponentially when subjected to PCR. Incontrast, the relatively large amount of hybrid molecules containingsequences held in common between tester and driver amplicons (i.e. onestrand was derived from the tester amplicon and one strand was derivedfrom the driver amplicon) will be amplified linearly when subjected toPCR. This is because only one strand (derived from the tester amplicon)contains the ligated adaptor sequence, and 3′ end filling will onlygenerate sequences complementary to the PCR primer on the strand derivedfrom the driver amplicon.

In step 5, the double-strand DNA of interest is enriched quantitativelyusing PCR for 10 cycles of amplification. As stated above in step 4,reannealed tester sequences will be amplified exponentially whereassequences held in common between tester and driver amplicons will beamplified linearly.

In step 6, single-strand DNA which remains is removed by a single strandDNA nuclease digestion using mung bean nuclease as described in the art.

In step 7, double-stranded DNA which remains after nuclease digestion isPCR amplified an additional 15 to 25 cycles.

Finally in step 8, these DNA products are cleaved with restrictionendonuclease to remove the oligonucleotide adaptors. These DNA productscan then be subjected to subsequent rounds of amplification (beginningat step #3 using the oligonucleotide adaptor set that was not used inthe previous cycle of RDA) or cloned into a suitable plasmid vector forfurther analysis.

The RDA procedure as described supra is a modification of therepresentational difference analysis known in the art. The method wasmodified to isolate viral clones from pre-inoculation and infectioussera sources. These modifications are discussed further below and relateto the preparation of amplicons for both tester and driver DNA. First,the starting material was not double-stranded DNA obtained from thegenomic DNA of mammalian cells as reported previously, but total nucleicacid extracted from infectious and pre-inoculation biological bloodsamples obtained from tamarins. It is possible that other biologicalsamples (for example, organs, tissue, bile, feces or urine) could beused as sources of nucleic acid from which tester and driver ampliconsare generated. Second, the amount of starting nucleic acid issubstantially less than that described in the art. Third, a restrictionendonuclease with a 4 bp instead of a 6 bp recognition site was used.This is substantially different from the prior art. Lisitsyn et al.teach that RDA works because the generation of amplicons (i.e.representations) decreases the complexity of the DNA that is beinghybridized (i.e. subtracted).

In the prior art, restriction enzymes that have 6 bp recognition siteswere used to fragment the genome. These restriction endonucleases cleaveapproximately every 4000 bp. However, the PCR conditions described inthe prior art amplify sequences ≦1500 bp in size. Therefore, subsequentPCR amplification of a complex species of DNA (such as a genome) thathas been fragmented with a restriction enzyme that recognizes a 6 bpsequence results in the generation of amplicons that contain thefraction of the DNA that was ≦1500 bp in size after restrictionendonuclease digestion. This reduction in DNA complexity (estimated tobe a 10- to 50-fold reduction) is reported to be necessary for thehybridization step of RDA to work. If the complexity is not reduced,unique sequences in the tester will not be able to efficiently hybridizeduring the subtraction step, and therefore, these unique sequences willnot be amplified exponentially during the subsequent PCR steps of RDA.

The reduction of complexity of the nucleic acid sequences beingsubjected to RDA undermines using RDA effectively to isolate relativelysmall viruses. The odds of two 6 bp-recognition sites occurring within1.5 kb of each other is sufficiently rare that one might miss a small(≦10 kb) virus (TABLE 1).

TABLE 1 Virus Enzyme # of Fragments <1.5 kb λ BamH I 0 (˜50 kb) Bgl II 3Hind III 1 Parvo B19 BamH I 0 (˜5 kb) Bgl II 0 Hind III 2 Sau3A I (4 bpsite) 5-7 HBV BamH I 1-2 (˜3.2 kb) Bgl II 1-2 Hind III 0 Sau3A I (4 bpsite) 12 

However, we have discovered that RDA may be useful in cloning smallviruses if a more frequently cutting restriction endonuclease is used tofragment the DNA being subjected to RDA. As shown in TABLE 1, ampliconsbased on 4 bp recognition site enzymes will almost certainly containseveral fragments from any small virus, as restriction endonucleaseswhich have 4 bp recognition sites fragment DNA approximately every 250base pairs. However, it is likely that amplicons will be as complex asthe source of the nucleic acid from which they were generated becausenearly all of the DNA species will be ≦1500 bp after digestion with a 4bp recognizing restriction endonuclease and thus, subject to PCRamplification. Since the relative viral sequence copy number ispredicted to be higher than any specific or endogenous sequence copynumber, the unique viral sequences that are present in the testeramplicon should be able to form double stranded molecules during thehybridization step (step 3, above). Therefore, these sequences will beamplified exponentially as described above. It is reasoned that as therelative viral sequence copy number becomes closer to that of thebackground or endogenous nucleic acid sequence copy number, arestriction endonuclease which recognizes a redundant 6 bp sequence (forexample BstYI or HincII) and cleaves approximately every 1000 bp, or thesimultaneous use of several restriction endonuclease which recognizes 6bp sequences, may be used to fragment the DNA prior to amplification byPCR. In this way, one can moderately reduce the complexity of theamplicons being subjected to RDA while minimizing the risk of excludingviral sequences from the tester amplicon. The utility of this procedureis demonstrated by the cloning of HGBV sequences from infectious tamarinplasma described herein.

Immunoscreening to Identify HGBV Immunoreactive Epitopes

Immunoscreening as described herein as follows also provided anadditional means of identifying HGBV sequences. Pooled or individualserum, plasma or liver homogenates from an individual meeting thecriteria and within the parameters set forth below with acute or chronicHGBV infection is used to isolate viral particles. Nucleic acidsisolated from these particles are used as the template in theconstruction of a genomic and/or cDNA library to the viral genome. Theprocedures used for isolation of putative HGBV particles and forconstructing the genonic and/or cDNA library in lambda-gt11 or similarsystems known in the art is discussed hereinbelow. Lambda-gt11 is avector that has been developed specifically to express inserted cDNAs asfusion polypeptides with beta-galactosidase and to screen large numbersof recombinant phage with specific antisera raised against a definedantigen. The lambda-gt11 cDNA library generated from a cDNA poolcontaining cDNA is screened for encoded epitopes that can bindspecifically with sera derived from individuals who previously hadexperienced non-A, non-B, non-C, non-D and non-E hepatitis. See V. Hunyhet al., in D. Glover, ed., DNA Cloning Techniques; A Practical Approach,IRL Press, Oxford, England, pp. 49-78 (1985). Approximately 10⁶-10⁷phage are screened, from which positive phage are identified, purified,and then tested for specificity of binding to sera from differentindividuals previously infected with the HGBV agent. Phage whichselectively bind sera or plasma from patients meeting the criteriadescribed hereinbelow and not in patients who did not meet thesedescribed criteria, are preferred for further study. By utilizing thetechnique of isolating overlapping nucleic acid sequences, clonescontaining additional upstream and downstream HGBV sequences areobtained. Analysis of the nucleotide sequences of the HGBV nucleic acidsequences encoded within the isolated clones is performed to determinewhether the composite sequence contains one long continuous ORF.

The sequences (and their complements) retrieved from the HGBV sequenceas provided herein, and the sequences or any portion thereof, can beprepared using synthetic methods or by a combination of syntheticmethods with retrieval of partial sequences using methods similar tothose described herein. This description thus provides one method bywhich genomic or cDNA sequences corresponding to the entire HGBV genomemay be isolated. Other methods for isolating these sequences, however,will be obvious to those skilled in the art and are considered to bewithin the scope of the present invention.

Deposit of Strains

Strains replicated (clones 2, 4, 10, 16, 18, 23 and 50) from the HGBVnucleic sequence library have been deposited at the American TypeCulture Collection, 10801 University Boulevard, Manassas, Va.20110-2209, as of Feb. 10, 1994, under the terms of the Budapest Treatyand will be maintained for a period of (30) years from the date ofdeposit, or for five (5) years after the last request for the deposit,or for the enforceable period of the U.S. patent, whichever is longer.The deposits and any other deposited material described herein areprovided for convenience only, and are not required to practice thepresent invention in view of the teachings provided herein. The HGBVcDNA sequences in all of the deposited materials are incorporated hereinby reference. The plasmids were accorded the following A.T.C.C. depositnumbers: Clone 2 was accorded A.T.C.C. Deposit No. 69556; Clone 4 wasaccorded A.T.C.C. Deposit No. 69557; Clone 10 was accorded A.T.C.C.Deposit No. 69558; Clone 16 was accorded A.T.C.C. Deposit No. 69559;Clone 18 was accorded A.T.C.C. Deposit No. 69560; Clone 23 was accordedA.T.C.C. Deposit No. 69561; and Clone 50 was accorded A.T.C.C. DepositNo. 69562.

Strains replicated (clones 11, 13, 48 and 119) from the HGBV nucleicacid sequence library have been deposited at the American Type CultureCollection, 10801 University Boulevard, Manassas, Va. 20110-2209, as ofApr. 29, 1994, under the terms of the Budapest Treaty and will bemaintained for a period of thirty (30) years from the date of deposit,or for five (5) years after the last request for the deposit, or for theenforceable period of the U.S. patent, whichever is longer. The depositsand any other deposited material described herein are provided forconvenience only, and are not required to practice the present inventionin view of the teachings provided herein. The HGBV cDNA sequences in allof the deposited materials are incorporated herein by reference. Theplasmids were accorded the following A.T.C.C. deposit numbers: Clone 11was accorded A.T.C.C. Deposit No. 69613; Clone 13 was accorded A.T.C.C.Deposit No. 69611; Clone 48 was accorded A.T.C.C. Deposit No. 69610; andClone 119 was accorded A.T.C.C. Deposit No. 69612.

Additional strains (clones 4-B1.1, 66-3A1.49, 70-3A1.37 and 78-1C1.17)from the HGBV nucleic acid sequence library have been deposited at theAmerican Type Culture Collection, 10801 University Boulevard, Manassas,Va. 20110-2209, as of Jul. 28, 1994, under the terms of the BudapestTreaty and will be maintained for a period of thirty (30) years from thedate of the deposit, or for five (5) years after the last request forthe deposit, or for the enforceable period of the U.S. patent, whicheveris longer. The deposits and anty other deposited mater described hereinare provided for convenience only, and are not required to practice thepresent invention in view of the teachings provided herein. The HGBVcDNA sequences in all of the deposited materials are incorporated hereinby reference. The plasmids were accorded the following A.T.C.C. depositnumbers: Clone 4-B1.1 was accorded A.T.C.C. Deposit No. 69666; Clone66-3A1.49 was accorded A.T.C.C. Deposit No. 69665; Clone 70-3A1.37 wasaccorded A.T.C.C. Deposit No. 69664; and Clone 78-1C1.17 was accordedA.T.C.C. Deposit No. 69663.

Clone pHGBV-C clone #1 was deposited at the American Type CultureCollection, 10801 University Boulevard, Manassas, Va. 20110-2209 as ofNov. 8, 1994, under the terms of the Budapest Treaty and will bemaintained for a period of thirty (30) years from the date of deposit,or for five (5) years after the last request for the deposit, or for theenforceable period of the U.S. patent, whichever is longer. The depositsand any other deposited material described herein are provided forconvenience only, and are not required to practice the invention in viewof the teachings provided herein. PHGBV-C clone #1 was accorded A.T.C.C.Deposit No. 69711. The HGBV cDNA sequences in all of the depositedmaterials are incorporated herein by reference.

Clone pHGBV-C clone #1 was deposited at the American Type CultureCollection, 12301 Parklawn Drive, Rockville, Md. 20852 as of Nov. 8,1994, under the terms of the Budapest Treaty and will be maintained fora period of thirty (30) years from the date of deposit, or for five (5)years after the last request for the deposit, or for the enforceableperiod of the U.S. patent, whichever is longer. The deposits and anyother deposited material described herein are provided for convenienceonly, and are not required to practice the present invention in view ofthe teachings provided herein. pHGBV-C clone #1 was accorded A.T.C.C.Deposit No. 69711. The HGBV cDNA sequences in all of the depositedmaterials are incorporated herein by reference.

Preparation of Viral Polypeptides and Fragments

The availability of nucleic acid sequences permits the construction ofexpression vectors encoding antigenically active regions of thepolypeptide encoded in either strand. These antigenically active regionsmay be derived from structural regions of the virus, including, forexample, envelope (coat) or core antigens, in addition to nonstructuralregions of the virus, including, for example, polynucleotide bindingproteins, polynucleotide polymerase(s), and other viral proteinsnecessary for replication and/or assembly of the viral particle.Fragments encoding the desired polypeptides are derived from the genomicor cDNA clones using conventional restriction digestion or by syntheticmethods, and are ligated into vectors which may, for example, containportions of fusion sequences such as beta-galactosidase (β-gal) orsuperoxide dismutase (SOD) or CMP-KDO synthetase (CKS). Methods andvectors which are useful for the production of polypeptides whichcontain fusion sequences of SOD are described in EPO 0196056, publishedOct. 1, 1986, and those of CKS are described in EPO Publication No.0331961, published Sep. 13, 1989. Any desired portion of the nucleicacid sequence containing an open reading frame, in either sense strand,can be obtained as a recombinant protein, such as a mature or fusionprotein; alternatively, a polypeptide encoded in the HGBV genome or cDNAcan be provided by chemical synthesis.

The nucleic acid sequence encoding the desired polypeptide, whether infused or mature form, and whether or not containing a signal sequence topermit secretion, may be ligated into expression vectors suitable forany convenient host. Both eucaryotic and prokaryotic host systems areused in the art to form recombinant proteins, and some of these arelisted herein. The polypeptide then is isolated from lysed cells or fromthe culture medium and purified to the extent needed for its intendeduse. Purification can be performed by techniques known in the art, andinclude salt fractionation, chromatography on ion exchange resins,affinity chromatography, centrifugation, among others. Such polypeptidesmay be used as diagnostic reagents, or for passive immunotherapy. Inaddition, antibodies to these polypeptides are useful for isolating andidentifying HGBV particles. The HGBV antigens also may be isolated fromHGBV virions. These virions can be grown in HGBV infected cells intissue culture, or in an infected individual.

Preparation of Antigenic Polypeptides and Conjugation with Solid Phase

An antigenic region or fragment of a polypeptide generally is relativelysmall, usually about 8 to 10 amino acids or less in length. Fragments ofas few as 5 amino acids may characterize an antigenic region. Thesesegments may correspond to regions of HGBV antigen. By using the HGBVgenomic or cDNA sequences as a basis, nucleic acid sequences encodingshort segments of HGBV polypeptides can be expressed recombinantlyeither as fusion proteins or as isolated polypeptides. These short aminoacid sequences also can be obtained by chemical synthesis. The smallchemically synthesized polypeptides may be linked to a suitable carriermolecule when the synthesized polypeptide provided is correctlyconfigured to provide the correct epitope but too small to be antigenic.Linking methods are known in the art and include but are not limited tousing N-succinimidyl-3-(2-pyrdylthio)propionate (SPDP) and succinimidyl4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC). Polypeptideslacking sulfhydryl groups can be modified by adding a cysteine residue.These reagents create a disulfide linkage between themselves and peptidecysteine residues on one protein and an amide linkage through theepsilon-amino on a lysine, or other free amino group in the other. Avariety of such disulfide/amide-forming agents are known. Otherbifunctional coupling agents form a thioester rather than a disulfidelinkage. Many of these thio-ether-forming agents are commerciallyavailable and are known to those of ordinary skill in the art. Thecarboxyl groups can be activated by combining them with succinimide or1-hydroxyl-2-nitro-4-sulfonic acid, sodium salt. Any carrier which doesnot itself induce the production of antibodies harmful to the host canbe used. Suitable carriers include proteins, polysaccharides such aslatex functionalized sepharose, agarose, cellulose, cellulose beads,polymeric amino acids such as polyglutamic acid, polylysine, amino acidcopolymers and inactive virus particles, among others. Examples ofprotein substrates include serum albumins, keyhole limpet hemocyanin,immunoglobulin molecules, thyroglobulin, ovalbumin, tetanus toxoid, andyet other proteins known to those skilled in the art.

Preparation of Hybrid Particle Immunogens Containing HGBV Epitopes

The immunogenicity of HGBV epitopes also may be enhanced by preparingthem in mammalian or yeast systems fused with or assembled withparticle-forming proteins such as those associated with HBV surfaceantigen. Constructs wherein the HGBV epitope is linked directly to theparticle-forming protein coding sequences produce hybrids which areimmunogenic with respect to the HGBV epitope. In addition, all of thevectors prepared include epitopes specific for HGBV, having varyingdegrees of immunogenicity. Particles constructed from particle formingprotein which include HGBV sequences are immunogenic with respect toHGBV and HBV.

Hepatitis B surface antigen has been determined to be formed andassembled into particles in S. cerevisiae and mammalian cells; theformation of these particles has been reported to enhance theimmunogenicity of the monomer subunit. P. Valenzuela et al., Nature298:334 (1982); P. Valenzuela et al., in I. Millman et al., eds.,Hepatitis B, Plenum Press, pp. 225-236 (1984). The constructs mayinclude immunodominant epitopes of HBsAg. Such constructs have beenreported expressible in yeast, and hybrids including heterologous viralsequences for yeast expression have been disclosed. See, for example,EPO 174, 444 and EPO 174,261. These constructs also have been reportedcapable of being expressed in mammalian cells such as Chinese hamsterovary (CHO) cells. Michelle et al., International Symposium on ViralHepatitis, 1984. In HGBV, portions of the particle-forming proteincoding sequence may be replaced with codons encoding an HGBV epitope. Inthis replacement, regions that are not required to mediate theaggregation of the units to form immunogenic particles in yeast ormammals can be deleted, thus eliminating additional HGBV antigenic sitesfrom competition with the HGBV epitope.

Vaccine Preparation

Vaccines may be prepared from one or more immunogenic polypeptides ornucleic acids derived from HGBV nucleic acid sequences or from the HGBVgenome to which they correspond. Vaccines may comprise recombinantpolypeptides containing epitope(s) of HGBV. These polypeptides may beexpressed in bacteria, yeast or mammalian cells, or alternatively may beisolated from viral preparations. It also is anticipated that variousstructural proteins may contain epitopes of HGBV which give rise toprotective anti-HGBV antibodies. Synthetic peptides therefore also canbe utilized when preparing these vaccines. Thus, polypeptides containingat least one epitope of HGBV may be used, either singly or incombinations, in HGBV vaccines. It also is contemplated thatnonstructural proteins as well as structural proteins may provideprotection against viral pathogenicity, even if they do not cause theproduction of neutralizing antibodies.

Considering the above, multivalent vaccines against HGBV may compriseone or more structural proteins, and/or one or more nonstructuralproteins. These vaccines may be comprised of, for example, recombinantHGBV polypeptides and/or polypeptides isolated from the virions and/orsynthetic peptides. These immunogenic epitopes can be used incombinations, i.e., as a mixture of recombinant proteins, syntheticpeptides and/or polypeptides isolated from the virion; these may beadministered at the same or different time. Additionally, it may bepossible to use inactivated HGBV in vaccines. Such inactivation may beby preparation of viral lysates, or by other means known in the art tocause inactivation of hepatitis-like viruses, for example, treatmentwith organic solvents or detergents, or treatment with formalin.Attenuated HGBV strain preparation also is disclosed in the presentinvention. It is contemplated that some of the proteins in HGBV maycross-react with other known viruses, and thus that shared epitopes mayexist between HGBV and other viruses which would then give rise toprotective antibodies against one or more of the disorders caused bythese pathogenic agents. It is contemplated that it may be possible todesign multiple purpose vaccines based upon this belief.

The preparation of vaccines which contain at least one immunogenicpeptide as an active ingredient is known to one skilled in the art.Typically, such vaccines are prepared as injectables, either as liquidsolutions or suspensions; solid forms suitable for solution in orsuspension in liquid prior to injection also may be prepared. Thepreparation may be emulsified or the protein may be encapsulated inliposomes. The active immunogenic ingredients often are mixed withpharmacologically acceptable excipients which are compatible with theactive ingredient. Suitable excipients include but are not limited towater, saline, dextrose, glycerol, ethanol and the like; combinations ofthese excipients in various amounts also may be used. The vaccine alsomay contain small amounts of auxiliary substances such as wetting oremulsifying reagents, pH buffering agents, and/or adjuvants whichenhance the effectiveness of the vaccine. For example, such adjuvantscan include aluminum hydroxide,N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-DMP),N-acetyl-nornuramyl-L-alanyl-D-isoglutamine (CGP 11687, also referred toas nor-MDP),N-acetylmuramyul-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′2′-dipalmitoyl-sn-glycero-3-hydroxphosphoryloxy)ethylamine(CGP 19835A, also referred to as MTP-PE), and RIBI (MPL+TDM+CWS) in a 2%squalene/Tween-80® emulsion. The effectiveness of an adjuvant may bedetermined by measuring the amount of antibodies directed against animmunogenic polypeptide containing an HGBV antigenic sequence resultingfrom administration of this polypeptide in vaccines which also arecomprised of the various adjuvants.

The vaccines usually are administered by intravenous or intramuscularinjection. Additional formulations which are suitable for other modes ofadministration include suppositories and, in some cases, oralformulations. For suppositories, traditional binders and carriers mayinclude but are not limited to polyalkylene glycols or triglycerides.Such suppositories may be formed from mixtures containing the activeingredient in the range of about 0.5% to about 10%, preferably, about 1%to about 2%. Oral formulation include such normally employed excipientsas, for example pharmaceutical grades of mannitol, lactose, starch,magnesium stearate, sodium saccharine, cellulose, magnesium carbonateand the like. These compositions may take the form of solutions,suspensions, tablets, pills, capsules, sustained release formulations orpowders and contain about 10% to about 95% of active ingredient,preferably about 25% to about 70%.

The proteins used in the vaccine may be formulated into the vaccine asneutral or salt forms. Pharmaceutically acceptable salts such as acidaddition salts (formed with free amino groups of the peptide) and whichare formed with inorganic acids such as hydrochloric or phosphoricacids, or such organic acids such as acetic, oxalic, tartaric, maleic,and others known to those skilled in the art. Salts formed with the freecarboxyl groups also may be derived from inorganic bases such as sodium,potassium, ammonium, calcium or ferric hydroxides and the like, and suchorganic bases such as isopropylamine, trimethylamine, 2-ethylaminoethanol, histidine procaine, and others known to those skilled in theart.

Vaccines are administered in a way compatible with the dosageformulation, and in such amounts as will be prophylactically and/ortherapeutically effective. The quantity to be administered generally isin the range of about 5 micrograms to about 250 micrograms of antigenper dose, and depends upon the subject to be dosed, the capacity of thesubject's immune system to synthesize antibodies, and the degree ofprotection sought. Precise amounts of active ingredient required to beadministered also may depend upon the judgment of the practitioner andmay be unique to each subject. The vaccine may be given in a single ormultiple dose schedule. A multiple dose is one in which a primary courseof vaccination may be with one to ten separate doses, followed by otherdoses given at subsequent time intervals required to maintain and/or toreinforce the immune response, for example, at one to four months for asecond dose, and if required by the individual, a subsequent dose(s)after several months. The dosage regimen also will be determined, atleast in part, by the need of the individual, and be dependent upon thepractitioner's judgment. It is contemplated that the vaccine containingthe immunogenic HGBV antigen(s) may be administered in conjunction withother immunoregulatory agents, for example, with immune globulins.

Preparation of Antibodies Against HGBV Epitopes

The immunogenic peptides prepared as described herein are used toproduce antibodies, either polyclonal or monoclonal. When preparingpolyclonal antibodies, a selected mammal (for example, a mouse, rabbit,goat, horse or the like) is immunized with an immunogenic polypeptidebearing at least one HGBV epitope. Serum from the immunized animal iscollected after an appropriate incubation period and treated accordingto known procedures. If serum containing polyclonal antibodies to anHGBV epitope contains antibodies to other antigens, the polyclonalantibodies can be purified by, for example, immunoaffinitychromatography. Techniques for producing and processing polyclonalantibodies are known in the art and are described in, among others,Mayer and Walker, eds., Immunochemical Methods In Cell and MolecularBiology, Academic Press, London (1987). Polyclonal antibodies also maybe obtained from a mammal previously infected with HGBV. An example of amethod for purifying antibodies to HGBV epitopes from serum of anindividual infected with HGBV using affinity chromatography is providedherein.

Monoclonal antibodies directed against HGBV epitopes also can beproduced by one skilled in the art. The general methodology forproducing such antibodies is well-known and has been described in, forexample, Kohler and Milstein, Nature 256:494 (1975) and reviewed in J.G. R. Hurrel, ed., Monoclonal Hybridoma Antibodies: Techniques andApplications, CRC Press Inc., Boco Raton, Fla. (1982), as well as thattaught by L. T. Mimms et al., Virology 176:604-619 (1990). Immortalantibody-producing cell lines can be created by cell fusion, and also byother techniques such as direct transformation of B lymphocytes withoncogenic DNA, or transfection with Epstein-Barr virus. See also, M.Schreier et al., Hybridoma Techniques, Scopes (1980) ProteinPurification, Principles and Practice, 2nd Edition, Springer-Verlag,N.Y. (1984); Hammerling et al., Monoclonal Antibodies and T-CellHybridomas (1981); Kennet et al., Monoclonal Antibodies (1980). Examplesof uses and techniques of monoclonal antibodies are disclosed in U.S.patent applications Ser. Nos. 748,292; 748,563; 610,175, 648,473;648,477; and 648,475.

Monoclonal and polyclonal antibodies thus developed, directed againstHGBV epitopes, are useful in diagnostic and prognostic applications, andalso, those which are neutralizing are useful in passive immunotherapy.Monoclonal antibodies especially can be used to produce anti-idiotypeantibodies. These anti-idiotype antibodies are immunoglobulins whichcarry an “internal image” of the antigen of the infectious agent againstwhich protection is desired. See, for example, A. Nisonoff et al., Clin.Immunol. Immunopath. 21:397-406 (1981), and Dreesman et al., J. Infect.Dis. 151:761 (1985). Techniques for raising such idiotype antibodies areknown in the art and exemplified, for example, in Grych et al., Nature316:74 (1985); MacNamara et al., Science 226:1325 (1984); and Uytdehaaget al., J. Immunol. 134:1225 (1985). These anti-idiotypic antibodiesalso may be useful for treatment of HGBV infection, as well as forelucidation of the immunogenic regions of HGBV antigens.

Diagnostic Oligonucleotide Probes and Kits

Using determined portions of the isolated HGBV nucleic acid sequences asa basis, oligomers of approximately eight nucleotides or more can beprepared, either by excision or synthetically, which hybridize with theHGBV genome and are useful in identification of the viral agent(s),further characterization of the viral genome, as well as in detection ofthe virus(es) in diseased individuals. The natural or derived probes forHGBV polynucleotides are a length which allows the detection of uniqueviral sequences by hybridization. While six to eight nucleotides may bea workable length, sequences of ten to twelve nucleotides are preferred,and those of about 20 nucleotides may be most preferred. These sequencespreferably will derive from regions which lack heterogeneity. Theseprobes can be prepared using routine, standard methods includingautomated oligonucleotide synthetic methods. A complement of any uniqueportion of the HGBV genome will be satisfactory. Completecomplementarity is desirable for use as probes, although it may beunnecessary as the length of the fragment is increased.

When used as diagnostic reagents, the test sample to be analyzed, suchas blood or serum, may be treated such as to extract the nucleic acidscontained therein. The resulting nucleic acid from the sample may besubjected to gel electrophoresis or other size separation techniques;or, the nucleic acid sample may be dot-blotted without size separation.The probes then are labeled. Suitable labels and methods for attachinglabels to probes are known in the art, and include but are not limitedto radioactive labels incorporated by nick translation or kinasing,biotin, fluorescent and chemiluminescent probes. Examples of many ofthese labels are disclosed herein. The nucleic acids extracted from thesample then are treated with the labeled probe under hybridizationconditions of suitable stringencies.

The probes can be made completely complementary to the HGBV genome.Therefore, usually high stringency conditions are desirable in order toprevent false positives. However, conditions of high stringency shouldbe used only if the probes are complementary to regions of the HGBVgenome which lack heterogeneity. The stringency of hybridization isdetermined by a number of factors during the washing procedure,including temperature, ionic strength, length of time and concentrationof formamide. See, for example, J. Sambrook (supra). Hybridization canbe carried out by a number of various techniques. Amplification can beperformed, for example, by Ligase Chain Reaction (LCR), Polymerase ChainReaction (PCR), Q-beta replicase, NASBA, etc.

It is contemplated that the HGBV genome sequences may be present inserum of infected individuals at relatively low levels, for example,approximately 10²-10³ sequences per ml. This level may require thatamplification techniques be used in hybridization assays, such as theLigase Chain Reaction or the Polymerase Chain Reaction. Such techniquesare known in the art. For example, the “Bio-Bridge” system uses terminaldeoxynucleotide transferase to add unmodified 3′-poly-dT-tails to anucleic acid probe (Enzo Biochem. Corp.). The poly dt-tailed probe ishybridized to the target nucleotide sequence, and then to abiotin-modified poly-A. Also, in EP 124221 there is described a DNAhybridization assay wherein the analyte is annealed to a single-strandedDNA probe that is complementary to an enzyme-labeled oligonucleotide,and the resulting tailed duplex is hybridized to an enzyme-labeledoligonucleotide. EP 204510 describes a DNA hybridization assay in whichanalyte DNA is contacted with a probe that has a tail, such as apoly-dT-tail, an amplifier strand that has a sequence that hybridizes tothe tail of the probe, such as a poly-A sequence, and which is capableof binding a plurality of labeled strands. The technique first mayinvolve amplification of the target HGBV sequences in sera toapproximately 10⁶ sequences/ml. This may be accomplished by followingthe methods described by Saiki et al., Nature 324:163 (1986). Theamplified sequence(s) then may be detected using a hybridization assaysuch as those known in the art. The probes can be packaged in diagnostickits which include the probe nucleic acid sequence which sequence may belabeled; alternatively, the probe may be unlabeled and the ingredientsfor labeling could be included with the kit. The kit also may containother suitably packaged reagents and materials needed or desirable forthe particular hybridization protocol, for example, standards as well asinstructions for performing the assay.

Other known amplification methods which can be utilized herein includebut are not limited to the so-called “NASBA” or “3SR” technique taughtin PNAS USA 87:1874-1878 (1990) and also discussed bin Nature:350 (No.6313):91-92 (1991) and Q-beta replicase.

Fluorescence in situ hybridization (“FISH”) also can be performedutilizing the reagents described herein. In situ hybridization involvestaking morphologically intact tissues, cells or chromosomes through thenucleic acid hybridization process to demonstrate the presence of aparticular piece of genetic information and its specific location withinindividual cells. Since it does not require homogenization of cells andextraction of the target sequence, it provides precise localization anddistribution of a sequence in cell populations. In situ hybridizationcan identify the sequence of interest concentrated in the cellscontaining it. It also can identify the type and fraction of the cellsin a heterogeneous cell population containing the sequence of interest.DNA and RNA can be detected with the same assay reagents. PNAs can beutilized in FISH methods to detect targets without the need foramplification. If increased signal is desired, multiple fluorophores canbe used to increase signal and thus, sensitivity of the method. Variousmethods of FISH are known, including a one-step method using multipleoligonucleotides or the conventional multi-step method. It is within thescope of the present invention that these types of methods can beautomated by various means including flow cytometry and image analysis.

Immunoassay and Diagnostic Kits

Both the polypeptides which react immunologically with serum containingHGBV antibodies and composites thereof, and the antibodies raisedagainst the HGBV specific epitopes in these polypeptides are useful inimmunoassays to detect the presence of HGBV antibodies, or the presenceof the virus and/or viral antigens in biological test samples. Thedesign of these immunoassays is subject to variation, and a variety ofthese are known in the art; a variety of these have been describedherein. The immunoassay may utilize one viral antigen, such as apolypeptide derived from any clone-containing HGBV nucleic acidsequence, or from the composite nucleic acid sequences derived from theHGBV nucleic acid sequences in these clones, or from the HGBV genomefrom which the nucleic acid sequences in these clones is derived. Or,the immunoassay may use a combination of viral antigens derived fromthese sources. It may use, for example, a monoclonal antibody directedagainst the same viral antigen, or polyclonal antibodies directedagainst different viral antigens. Assays can include but are not limitedto those based on competition, direct reaction or sandwich-type assays.Assays may use solid phases or may be performed by immunoprecipitationor any other methods which do not utilize solid phases. Examples ofassays which utilize labels as the signal generating compound and thoselabels are described herein. Signals also may be amplified by usingbiotin and avidin, enzyme labels or biotin anti-biotin systems, such asthat described in pending U.S. patent application Ser. Nos. 608,849;070,647; 418,981; and 687,785. Recombinant polypeptides which includeepitopes from immunodominant regions of HGBV may be useful for thedetection of viral antibodies in biological test samples of infectedindividuals. It also is contemplated that antibodies may be useful indiscriminating acute from non-acute infections. Kits suitable forimmunodiagnosis and containing the appropriate reagents are constructedby packaging the appropriate materials, including the polypeptides ofthe invention containing HGBV epitopes or antibodies directed againstHGBV epitopes in suitable containers, along with the remaining reagentsand materials required for the conduct of the assay, as well as suitableassay instructions.

Assay formats can be designed which utilize the recombinant proteinsdetailed herein, and although we describe and detail CKS proteins, italso is contemplated that other expression systems, such as superoxidedismutase (SOD), and others, can be used in the present invention togenerate fusion proteins capable of use in a variety of ways, includingas antigens in immunoassays, immunogens for antibody production, and thelike. In an assay format to detect the presence of antibody against aspecific analyte (for example, an infectious agent such as a virus) in ahuman test sample, the human test sample is contacted and incubated witha solid phase coated with at least one recombinant protein(polypeptide). If antibodies are present in the test sample, they willform a complex with the antigenic polypeptide and become affixed to thesolid phase. After the complex has formed, unbound materials andreagents are removed by washing the solid phase. The complex is reactedwith an indicator reagent and allowed to incubate for a time and underconditions for second complexes to form. The presence of antibody in thetest sample to the CKS recombinant polypeptide(s) is determined bydetecting the signal generated. Signal generated above a cut-off valueis indicative of antibody to the analyte present in the test sample.With many indicator reagents, such as enzymes, the amount of antibodypresent is proportional to the signal generated. Depending upon the typeof test sample, it may be diluted with a suitable buffer reagent,concentrated, or contacted with the solid phase without any manipulation(“neat”). For example, it usually is preferred to test serum or plasmasamples which previously have been diluted, or concentrate specimenssuch as urine, in order to determine the presence and/or amount ofantibody present.

In addition, more than one recombinant protein can be used in the assayformat just described to test for the presence of antibody against aspecific infectious agent by utilizing CKS fusion proteins againstvarious antigenic epitopes of the viral genome of the infectious agentunder study. Thus, it may be preferred to use recombinant polypeptideswhich contain epitopes within a specific viral antigenic region as wellas epitopes from other antigenic regions from the viral genome toprovide assays which have increased sensitivity and perhaps greaterspecificity than using a polypeptide from one epitope. Such an assay canbe utilized as a confirmatory assay. In this particular assay format, aknown amount of test sample is contacted with (a) known amount(s) of atleast one solid support coated with at least one recombinant protein fora time and under conditions sufficient to form recombinantprotein/antibody complexes. The complexes are contacted with knownamount(s) of appropriate indicator reagent(s)s for a time and undersuitable conditions for a reaction to occur, wherein the resultantsignal generated is compared to a negative test sample in order todetermine the presence of antibody to the analyte in the test sample. Itfurther is contemplated that, when using certain solid phases such asmicroparticles, each recombinant protein utilized in the assay can beattached to a separate microparticle, and a mixture of thesemicroparticles made by combining the various coated microparticles,which can be optimized for each assay.

Variations to the above-described assay formats include theincorporation of CKS-recombinant proteins of different analytes attachedto the same or to different solid phases for the detection of thepresence of antibody to either analyte (for example, CKS-recombinantproteins specific for certain antigenic regions of one infective agentcoated on the same or different solid phase with CKS-recombinantproteins specific for certain antigenic region(s) of a differentinfective agent, to detect the presence of either (or both) infectiveagents.

In yet another assay format, CKS recombinant proteins containingantigenic epitopes are useful in competitive assays such asneutralization assays. To perform a neutralization assay, a recombinantpolypeptide representing epitopes of an antigenic region of aninfectious agent such as a virus, is solubilized and mixed with a samplediluent to a final concentration of between 0.5 to 50.0 μg/ml. A knownamount of test sample (preferably 10 μl), either diluted or non-diluted,is added to a reaction well, followed by 400 μl of the sample diluentcontaining the recombinant polypeptide. If desired, the mixture may bepreincubated for approximately 15 minutes to two hours. A solid phasecoated with the CKS recombinant protein described herein then is addedto the reaction well, and incubated for one hour at approximately 40° C.After washing, a known amount of an indicator reagent, for example, 200μl of a peroxidase labeled goat anti-human IgG in a conjugate diluent isadded and incubated for one hour at 40° C. After washing and when usingan enzyme conjugate such as described, an enzyme substrate, for example,OPD substrate, is added and incubated at room temperature for thirtyminutes. The reaction is terminated by adding a stopping reagent such as1N sulfuric acid to the reaction well. Absorbance is read at 492 nm.Test samples which contain antibody to the specific polypeptide generatea reduced signal caused by the competitive binding of the peptides tothese antibodies in solution. The percentage of competitive binding maybe calculated by comparing absorbance value of the sample in thepresence of recombinant polypeptide to the absorbance value of thesample assayed in the absence of a recombinant polypeptide at the samedilution. Thus, the difference in the signals generated between thesample in the presence of recombinant protein and the sample in theabsence of recombinant protein is the measurement used to determine thepresence or absence of antibody.

In another assay format, the recombinant proteins can be used inimmunodot blot assay systems. The immunodot blot assay system uses apanel of purified recombinant polypeptides placed in an array on anitrocellulose solid support. The prepared solid support is contactedwith a sample and captures specific antibodies (specific binding member)to the recombinant protein (other specific binding member) to formspecific binding member pairs. The captured antibodies are detected byreaction with an indicator reagent. Preferably, the conjugate specificreaction is quantified using a reflectance optics assembly within aninstrument which has been described in U.S. patent application Ser. No.07/227,408 filed Aug. 2, 1988. The related U.S. patent application Ser.Nos. 07/227,586 and 07/227.590 (both of which were filed on Aug. 2,1988) further described specific methods and apparatus useful to performan immunodot assay, as well as U.S. Pat. No. 5,075,077 (U.S. Ser. No.07/227,272 filed Aug. 2, 1988), which enjoys common ownership and isincorporated herein by reference. Briefly, a nitrocellulose-base testcartridge is treated with multiple antigenic polypeptides. Eachpolypeptide is contained within a specific reaction zone on the testcartridge. After all the antigenic polypeptides have been placed on thenitrocellulose, excess binding sites on the nitrocellulose are blocked.The test cartridge then is contacted with a test sample such that eachantigenic polypeptide in each reaction zone will react if the testsample contains the appropriate antibody. After reaction, the testcartridge is washed and any antigen-antibody reactions are identifiedusing suitable well-known reagents. As described in the patents andpatent applications listed herein, the entire process is amenable toautomation. The specifications of these applications related to themethod and apparatus for performing an immunodot blot assay areincorporated herein by reference.

CKS fusion proteins can be used in assays which employ a first andsecond solid support, as follow, for detecting antibody to a specificantigen of an analyte in a test sample. In this assay format, a firstaliquot of a test sample is contacted with a first solid support coatedwith CKS recombinant protein specific for an analyte for a time andunder conditions sufficient to form recombinant protein/analyte antibodycomplexes. Then, the complexes are contacted with an indicator reagentspecific for the recombinant antigen. The indicator reagent is detectedto determine the presence of antibody to the recombinant protein in thetest sample. Following this, the presence of a different antigenicdeterminant of the same analyte is determined by contacting a secondaliquot of a test sample with a second solid support coated with CKSrecombinant protein specific for the second antibody for a time andunder conditions sufficient to form recombinant protein/second antibodycomplexes. The complexes are contacted with a second indicator reagentspecific for the antibody of the complex. The signal is detected inorder to determine the presence of antibody in the test sample, whereinthe presence of antibody to either analyte recombinant protein, or both,indicates the presence of anti-analyte in the test sample. It also iscontemplated that the solid supports can be tested simultaneously.

The use of haptens is known in the art. It is contemplated that haptensalso can be used in assays employing CKS fusion proteins in order toenhance performance of the assay.

Further Characterization of the HGBV Genome, Virions, and Viral AntigensUsing Probes

The HGBV nucleic acid sequences may be used to gain further informationon the sequence of the HGBV genome, and for identification and isolationof the HGBV agent. Thus, it is contemplated that this knowledge will aidin the characterization of HGBV including the nature of the HGBV genome,the structure of the viral particle, and the nature of the antigens ofwhich it is composed. This information, in turn, can lead to additionalpolynucleotide probes, polypeptides derived from the HGBV genome, andantibodies directed against HGBV epitopes which would be useful for thediagnosis and/or treatment of HGBV caused non-A, non-B, non-C, non-D andnon-E hepatitis.

The nucleic acid sequence information is useful for the design of probesor PCR primers for the isolation of additional nucleic acid sequenceswhich are derived from yet undefined regions of the HGBV genome. Forexample, PCR primers or labeled probes containing a sequence of 8 ormore nucleotides, and preferably 20 or more nucleotides, which arederived from regions close to the 5′-termini or 3′-termini of the familyof HGBV nucleic acid sequences may be used to isolate overlappingnucleic acid sequences from HGBV genomic or cDNA libraries or directlyfrom viral nucleic acid. These sequences which overlap the HGBV nucleicacid sequences, but which also contain sequences derived from regions ofthe genome from which the above-mentioned HGBV nucleic acid sequence arenot derived, may then be used to synthesize probes for identification ofother overlapping fragments which do not necessarily overlap the nucleicacid sequences in the clones. Unless the HGBV genome is segmented andthe segments lack common sequences, it is possible to sequence theentire viral genome(s) utilizing the technique of isolation ofoverlapping nucleic acid sequences derived from the viral genome(s).Characterization of the genomic segments alternatively could be from theviral genome(s) isolated from purified HGBV particles. Methods forpurifying HGBV particles and for detecting them during the purificationprocedure are described herein. Procedures for isolating polynucleotidegenomes from viral particles are well-known in the art. The isolatedgenomic segments then could be cloned and sequenced. Thus, it ispossible to clone and sequence the HGBV genome(s) irrespective of theirnature.

Methods for constructing HGBV genomic or cDNA libraries are known in theart, and vectors useful for this purpose are known in the art. Thesevectors include lambda-gt11, lambda-gt10, and others. The HGBV derivednucleic acid sequence detected by the probes derived from the HGBVgenomic or cDNAs, may be isolated from the clone by digestion of theisolated polynucleotide with the appropriate restriction enzyme(s), andsequenced.

The sequence information derived from these overlapping HGBV nucleicacid sequences is useful for determining areas of homology andheterogeneity within the viral genome(s), which could indicate thepresence of different strains of the genome and or of populations ofdefective particles. It is also useful for the design of hybridizationprobes to detect HGBV or HGBV antigens or HGBV nucleic acids inbiological samples, and during the isolation of HGBV, utilizing thetechniques described herein. The overlapping nucleic acid sequences maybe used to create expression vectors for polypeptides derived from theHGBV genome(s). Encoded within the family of nucleic acid sequences areantigen(s) containing epitopes which are contemplated to be unique toHGBV, i.e., antibodies directed against these antigens are absent fromindividuals infected with HAV, HBV, HCV, and HEV, and with the genomicsequences in GenBank are contemplated to indicate that minimal homologyexists between these nucleic acid sequences and the polynucleotidesequences of those sources. Thus, antibodies directed against theantigens encoded with the HGBV nucleic acid sequences may be used toidentify the non-A, non-B, non-C, non-D and non-E particle isolated frominfected individuals. In addition, they also are useful for theisolation of the HGBV agent(s).

HGBV particles may be isolated from the sera of infected individuals orfrom cell cultures by any of the methods known in the art, including,for example, techniques based on size discrimination such assedimentation or exclusion methods, or techniques based on density suchas ultracentrifugation in density gradients, or precipitation withagents such as polyethylene glycol (PEG), or chromatography on a varietyof materials such as anionic or cationic exchange materials, andmaterials which bind due to hydrophobic interactions, as well asaffinity columns. During the isolation procedure the presence of HGBVmay be detected by hybridization analysis of the extracted genome, usingprobes derived from HGBV nucleic acid sequences or by immunoassay whichutilize as probes antibodies directed against HGBV antigens encodedwithin the family of HGBV nucleic acid sequences. The antibodies may bepolyclonal or monoclonal, and it may be desirable to purify theantibodies before their use in the immunoassay. Such antibodies directedagainst HGBV antigens which are affixed to solid phases are useful forthe isolation of HGBV by immunoaffinity chromatography. Methods forimmunoaffinity chromatography are known in the art, and include methodsfor affixing antibodies to solid phases so that they retain theirimmunoselective activity. These methods include adsorption, and covalentbinding. Spacer groups may be included in the bifunctional couplingagents such that the antigen binding site of the antibody remainsaccessible.

During the purification procedure the presence of HGBV may be detectedand/or verified by nucleic acid hybridization or PCR, utilizing asprobes or primers polynucleotides derived from a family of HGBV genomicor cDNA sequences, as well as from overlapping HGBV nucleic acidsequences. Fractions are treated under conditions which would cause thedisruption of viral particles, such as by use of detergents in thepresence of chelating agents, and the presence of viral nucleic aciddetermined by hybridization techniques or PCR. Further confirmation thatthe isolated particles are the agents which induce HGBV infection may beobtained by infecting an individual which is preferably a tamarin withthe isolated virus particles, followed by a determination of whether thesymptoms of non-A, non-B, non-C, non-D and non-E hepatitis, as describedherein, result from the infection.

Such viral particles obtained from the purified preparations then may befurther characterized. The genomic nucleic acid, once purified, can betested to determine its sensitivity to RNAse or DNAse I; based on thesetests, the determination of HGBV as a RNA genome or DNA genome may bemade. The strandedness and circularity or non-circularity can bedetermined by methods known in the art including its visualization byelectron microscopy, its migration in density gradients and itssedimentation characteristics. From hybridization of the HGBV genome,the negative or positive strandedness of the purified nucleic acid canbe determined. In addition, the purified nucleic acid can be cloned andsequenced by known techniques, including reverse transcriptase, if thegenomic material is RNA. Utilizing the nucleic acid derived from theviral particles, it then is possible to sequence the entire genome,whether or not it is segmented.

Determination of polypeptides containing conserved sequences may beuseful for selecting probes which bind the HGBV genome, thus allowingits isolation. In addition, conserved sequences in conjunction withthose derived from the HGBV nucleic acid sequences, may be used todesign primers for use in systems which amplify genomic sequences.Further, the structure of HGBV also may be determined and its componentsisolated. The morphology and size may be determined by electronmicroscopy, for example. The identification and localization of specificviral polypeptide antigens such as envelope (coat) antigens, or internalantigens such as nucleic acid binding proteins or core antigens, andpolynucleotide polymerase(s) also may be determined by ascertainingwhether the antigens are present in major or minor viral components, aswell as by utilizing antibodies directed against the specific antigensencoded within isolated nucleic acid sequences as probes. Thisinformation may be useful for diagnostic and therapeutic applications.For example, it may be preferable to include an exterior antigen in avaccine preparation, or perhaps multivalent vaccines may be comprised ofa polypeptide derived from the genome encoding a structural protein aswell as a polypeptide from another portion of the genome, such as anonstructural polypeptide.

Cell Culture Systems and Animal Model Systems for HGBV Replication

Generally, suitable cells or cell lines for culturing HGBV may includethe following: monkey kidney cells such as MK2 and VERO, porcine kidneycell lines such as PS, baby hamster kidney cell lines such as BHK,murine macrophage cell lines such as P388D1, MK1 and Mm1, humanmacrophage cell lines such as U-937, human peripheral blood leukocytes,human adherent monocytes, hepatocytes or hepatocytic cell lines such asHUH7 and HepG2, embryos or embryonic cell such as chick embryofibroblasts or cell lines derived from invertebrates, preferably frominsects such as Drosophia cell lines or more preferably from arthropodssuch as mosquito cell lines or tick cell lines It also is possible thatprimary hepatocytes can be cultured and then infected with HGBV.Alternatively, the hepatocyte cultures could be derived from the liversof infected individuals (human or tamarins). That latter case is anexample of a cell line which is infected in vivo being passaged invitro. In addition, various immortalization methods can be used toobtain cell lines derived from hepatocyte cultures. For example, primaryliver cultures (before and after enrichment of the hepatocytepopulation) may be fused to a variety of cells to maintain stability.Also, cultures may be infected with transforming viruses, or transfectedwith transforming genes in order to create permanent or semipermanentcell lines. In addition, cells in liver cultures may be fused toestablished cell lines such as PehG2. Methods for cell fusion arewell-known to the routineer, and include the use of fusion agents suchas PEG and Sendai Virus, among others.

It is contemplated that HGBV infection of cell lines may be accomplishedby techniques such as incubating the cells with viral preparations underconditions which allow viral entry into the cell. It also may bepossible to obtain viral production by transfecting the cells withisolated viral polynucleotides. Methods for transfecting tissue culturecells are known in the art and include but are not limited to techniqueswhich use electroporation and precipitation with DEAE-Dextran or calciumphosphate. Transfection with cloned HGBV genomic or cDNA should resultin viral replication and the in vitro propagation of the virus. Inaddition to cultured cells, animal model systems may be used for viralreplication. HGBV replication thus may occur in chimpanzees and also in,for example, marmosets and suckling mice.

Screening for Anti-Viral Agents for HGBV

The availability of cell culture and animal model systems for HGBV alsorenders screening for anti-viral agents which inhibit HGBV replicationpossible, and particularly for those agents which preferentially allowcell growth and multiplication while inhibiting viral replication. Thesescreening methods are known in the art. Generally, the anti-viral agentsare tested at a variety of concentrations, for their effect onpreventing viral replication in cell culture systems which support viralreplication, and then for an inhibition of infectivity or of viralpathogenicity, and a low level of toxicity, in an animal model system.The methods and composition provided herein for detecting HGBV antigensand HGBV polynucleotides are useful for screening of anti-viral agentsbecause they provide an alternative, and perhaps a more sensitive means,for detecting the agent's effect on viral replication than the cellplaque assay or ID₅₀ assay. For example, the HGBV polynucleotide probesdescribed herein may be used to quantitate the amount of viral nucleicacid produced in a cell culture. This could be performed byhybridization or competition hybridization of the infected cell nucleicacids with a labeled HGBV polynucleotide probe. Also, anti-HGBVantibodies may be used to identify and quantitate HGBV antigen(s) in thecell culture utilizing the immunoassays described herein. Also, since itmay be desirable to quantitate HGBV antigens in the infected cellculture by a competition assay, the polypeptides encoded within the HGBVnucleic acid sequences described herein are useful for these assays.Generally, a recombinant HGBV polypeptide derived from the HGBV genomicor cDNA would be labeled, and the inhibition of binding of this labeledpolypeptide to an HGBV polypeptide due to the antigen produced in thecell culture system would be monitored. These methods are especiallyuseful in cases where the HGBV may be able to replicate in a cell lineswithout causing cell death.

Preparation of Attenuated Strains of HGBV

It may be possible to isolate attenuated strains of HGBV by utilizingthe tissue culture systems and/or animal models systems provided herein.These attenuated strains would be useful for vaccines, or for theisolation of viral antigens. Attenuated strains are isolatable aftermultiple passages in cell culture and/or an animal model. Detection ofan attenuated strain in an infected cell or individual is achievable byfollowing methods known in the art and could include the use ofantibodies to one or more epitopes encoded in HGBV as a probe or the useof a polynucleotide containing an HGBV sequence of at least about 8nucleotides in length as a probe. Also or alternatively, an attenuatedstrain may be constructed utilizing the genomic information of HGBVprovided herein, and utilizing recombinant techniques. Usually anattempt is made to delete a region of the genome encoding a polypeptiderelated to pathogenicity but not to viral replication. The genomicconstruction would allow the expression of an epitope which gives riseto neutralizing antibodies for HGBV. The altered genome then could beused to transform cells which allow HGBV replication, and the cellsgrown under conditions to allow viral replication. Attenuated HGBVstrains are useful not only for vaccine purposes, but also as sourcesfor the commercial production of viral antigens, since the processing ofthese viruses would require less stringent protection measures for theemployees involved in viral production and/or the production of viralproducts.

Hosts and Expression Control Sequences

Although the following are known in the art, included herein are generaltechniques used in extracting the genome from a virus, preparing andprobing a genomic library, sequencing clones, constructing expressionvectors, transforming cells, performing immunological assays, and forgrowing cell in culture.

Both prokaryotic and eukaryotic host cells may be used for expression ofdesired coding sequences when appropriate control sequences which arecompatible with the designated host are used. Among prokaryotic hosts,E. coli is most frequently used. Expression control sequences forprokaryotics include promoters, optionally containing operator portions,and ribosome binding sites. Transfer vectors compatible with prokaryotichosts are commonly derived from the plasmid pBR322 which containsoperons conferring ampicillin and tetracycline resistance, and thevarious pUC vectors, which also contain sequences conferring antibioticresistance markers. These markers may be used to obtain successfultransformants by selection. Commonly used prokaryotic control sequencesinclude the beta-lactamase (penicillinase), lactose promoter system(Chang et al., Nature 198:1056 [1977]) the tryptophan promoter system(reported by Goeddel et al., Nucleic Acid Res 8:4057 [1980]) and thelambda-derived P1 promoter and N gene ribosome binding site (Shimatakeet al., Nature 292:128 [1981]) and the hybrid Tac promoter (De Boer etal., Proc. Natl. Acad. Sci. USA 292:128 [1983]) derived from sequencesof the trp and lac UV5 promoters. The foregoing systems are particularlycompatible with E. coli; however, other prokaryotic hosts such asstrains of Bacillus or Pseudomonas may be used if desired, withcorresponding control sequences.

Eukaryotic hosts include yeast and mammalian cells in culture systems.Saccharomyces cerevisiae and Saccharomyces carlsbergensis are the mostcommonly used yeast hosts, and are convenient fungal hosts. Yeastcompatible vectors carry markers which permit selection of successfultransformants by conferring protrophy to auxotrophic mutants orresistance to heavy metals on wild-type strains. Yeast compatiblevectors may employ the 2 micron origin of replication (as described byBroach et al., Meth. Enz. 101:307 [1983]), the combination of CEN3 andARS1 or other means for assuring replication, such as sequences whichwill result in incorporation of an appropriate fragment into the hostcell genome. Control sequences for yeast vectors are known in the artand include promoters for the synthesis of glycolytic enzymes, includingthe promoter for 3 phosphophycerate kinase. See, for example, Hess etal., J. Adv. Enzyme Reg. 7: 149 (1968), Holland et al., Biochemistry17:4900 (1978) and Hitzeman J. Biol. Chem. 255:2073 (1980). Terminatorsalso may be included, such as those derived from the enolase gene asreported by Holland, J. Biol. Chem. 256:1385 (1981). It is contemplatedthat particularly useful control systems are those which comprise theglyceraldehyde-3 phosphate dehydrogenase (GAPDH) promoter or alcoholdehydrogenase (ADH) regulatable promoter, terminators also derived fromGAPDH, and if secretion is desired, leader sequences from yeast alphafactor. In addition, the transcriptional regulatory region and thetranscriptional initiation region which are operably linked may be suchthat they are not naturally associated in the wild-type organism.

Mammalian cell lines available as hosts for expression are known in theart and include many immortalized cell lines which are available fromthe American Type Culture Collection. These include HeLa cells, Chinesehamster ovary (CHO) cells, baby hamster kidney (BHK) cells, and others.Suitable promoters for mammalian cells also are known in the art andinclude viral promoters such as that from Simian Virus 40 (SV40), Roussarcoma virus (RSV), adenovirus (ADV), bovine papilloma virus (BPV),cytomegalovirus (CMV). Mammalian cells also may require terminatorsequences and poly A addition sequences; enhancer sequences whichincrease expression also may be included, and sequences which causeamplification of the gene also may be desirable. These sequences areknown in the art. Vectors suitable for replication in mammalian cellsmay include viral replicons, or sequences which insure integration ofthe appropriate sequences encoding non-A, non-B, non-C, non-D, non-Eepitopes into the host genome. An example of a mammalian expressionsystem for HCV is described in U.S. patent application Ser. No.07/830,024, filed Jan. 31, 1992.

Transformations

Transformation may be by any known method for introducingpolynucleotides into a host cell, including packaging the polynucleotidein a virus and transducing a host cell with the virus, and by directuptake of the polynucleotide. The transformation procedures selecteddepends upon the host to be transformed. Bacterial transformation bydirect uptake generally employs treatment with calcium or rubidiumchloride. Cohen, Proc. Natl. Acad. Sci. USA 69:2110 (1972). Yeasttransformation by direct uptake may be conducted using the calciumphosphate precipitation method of Graham et al., Virology 52:526 (1978),or modification thereof.

Vector Construction

Vector construction employs methods known in the art. Generally,site-specific DNA cleavage is performed by treating with suitablerestriction enzymes under conditions which generally are specified bythe manufacturer of these commercially available enzymes. Usually, about1 microgram (μg) of plasmid or DNA sequence is cleaved by 1-10 units ofenzyme in about 20 μl of buffer solution by incubation at 37° C. for 1to 2 hours. After incubation with the restriction enzyme, protein isremoved by phenol/chloroform extraction and the DNA recovered byprecipitation with ethanol. The cleaved fragments may be separated usingpolyacrylamide or agarose gel electrophoresis methods, according tomethods known by the routineer.

Sticky end cleavage fragments may be blunt ended using E. coli DNApolymerase 1 (Klenow) in the presence of the appropriate deoxynucleotidetriphosphates (dNTPs) present in the mixture. Treatment with S1 nucleasealso may be used, resulting in the hydrolysis of any single stranded DNAportions.

Ligations are performed using standard buffer and temperature conditionsusing T4 DNA ligase and ATP. Sticky end ligations require less ATP andless ligase than blunt end ligations. When vector fragments are used aspart of a ligation mixture, the vector fragment often is treated withbacterial alkaline phosphatase (BAP) or calf intestinal alkalinephosphatase to remove the 5′-phosphate and thus prevent religation ofthe vector. Or, restriction enzyme digestion of unwanted fragments canbe used to prevent ligation. Ligation mixtures are transformed intosuitable cloning hosts such as E. coli and successful transformantsselected by methods including antibiotic resistance, and then screenedfor the correct construction.

Construction of Desired DNA Sequences

Synthetic oligonucleotides may be prepared using an automatedoligonucleotide synthesizer such as that described by Warner, DNA 3:401(1984). If desired, the synthetic strands may be labeled with ³²P bytreatment with polynucleotide kinase in the presence of ³²P-ATP, usingstandard conditions for the reaction. DNA sequences including thoseisolated from genomic or cDNA libraries, may be modified by knownmethods which include site directed mutagenesis as described by Zoller,Nucleic Acids Res. 10:6487 (1982). Briefly, the DNA to be modified ispackaged into phage as a single stranded sequence, and converted to adouble stranded DNA with DNA polymerase using, as a primer, a syntheticoligonucleotide complementary to the portion of the DNA to be modified,and having the desired modification included in its own sequence.Culture of the transformed bacteria, which contain replications of eachstrand of the phage, are plated in agar to obtain plaques.Theoretically, 50% of the new plaques contain phage having the mutatedsequence, and the remaining 50% have the original sequence. Replicatesof the plaques are hybridized to labeled synthetic probe at temperaturesand conditions suitable for hybridization with the correct strand, butnot with the unmodified sequence. The sequences which have beenidentified by hybridization are recovered and cloned.

Hybridization with Probe

HGBV genomic or DNA libraries may be probed using the proceduredescribed by Grunstein and Hogness, Proc. Natl. Acad. Sci. USA 73:3961(1975). Briefly, the DNA to be probed is immobilized on nitrocellulosefilters, denatured and prehybridized with a buffer which contains 0-50%formamide, 0.75 M NaCl, 75 mM Na citrate, 0.02% (w/v) each of bovineserum albumin (BSA), polyvinyl pyrollidone and Ficoll, 50 mM NaPhosphate (pH 6.5), 0.1% SDS and 100 μg/ml carrier denatured DNA. Thepercentage of formamide in the buffer, as well as the time andtemperature conditions of the prehybridization and subsequenthybridization steps depends on the stringency required. Oligomericprobes which require lower stringency conditions are generally used withlow percentages of formamide, lower temperatures, and longerhybridization times. Probes containing more than 30 or 40 nucleotidessuch as those derived from cDNA or genomic sequences generally employhigher temperatures, for example, about 40 to 42° C., and a highpercentage, for example, 50% formamide. Following prehybridization, a³²P-labeled oligonucleotide probe is added to the buffer, and thefilters are incubated in this mixture under hybridization conditions.After washing, the treated filters are subjected to autoradiography toshow the location of the hybridized probe. DNA in correspondinglocations on the original agar plates is used as the source of thedesired DNA.

Verification of Construction and Sequencing

For standard vector constructions, ligation mixtures are transformedinto E. coli strain XL-1 Blue or other suitable host, and successfultransformants selected by antibiotic resistance or other markers.Plasmids from the transformants then are prepared according to themethod of Clewell et al., Proc. Natl. Acad. Sci. USA 62:1159 (1969)usually following chloramphenicol amplification as reported by Clewellet al., J. Bacteriol. 110:667 (1972). The DNA is isolated and analyzedusually by restriction enzyme analysis and/or sequencing. Sequencing maybe by the well-known dideoxy method of Sanger et al., Proc. Natl. Acad.Sci. USA 74:5463 (1977) as further described by Messing et al., NucleicAcid Res. 9:309 (1981), or by the method reported by Maxam et al.,Methods in Enzymology 65:499 (1980). Problems with band compression,which are sometimes observed in GC rich regions, are overcome by use ofT-deazoguanosine according to the method reported by Barr et al.,Biotechniques 4:428 (1986).

Enzyme-Linked Immunosorbent Assay

Enzyme-linked immunosorbent assay (ELISA) can be used to measure eitherantigen or antibody concentrations. This method depends upon conjugationof an enzyme label to either an antigen or antibody, and uses the boundenzyme activity (signal generated) as a quantitative label (measurablegenerated signal). Methods which utilize enzymes as labels are describedherein, as are examples of such enzyme labels.

Preparation of HGBV Nucleic Acid Sequences

The source of the non-A, non-B, non-C, non-D, non-E agent is anindividual or pooled plasma, serum or liver homogenate from a human ortamarin infected with the HGBV virus meeting the clinical and laboratorycriteria described herein. A tamarin alternatively can be experimentallyinfected with blood from another individual with non-A, non-B, non-C,non-E hepatitis meeting the criteria described hereinbelow. A pool canbe made by combining many individual plasma, serum or liver homogenatesamples containing high levels of alanine transferase activity; thisactivity results from hepatic injury due to HGBV infection. The TID(tamarin infective dose) of the virus has been calculated from one ofour experiments to be ≧4×10⁵/ml (see Example 2, below).

For example, a nucleic acid library from plasma, serum or liverhomogenate, preferably but not necessarily high titer, is generated asfollows. First, viral particles are isolated from the plasma, serum orliver homogenate; then an aliquot is diluted in a buffered solution,such as one containing 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, 100 mM NaCl.Debris is removed by centrifugation, for example, for 20 minutes at15,000×g at 20° C. Viral particles in the resulting supernatant then arepelleted by centrifugation under appropriate conditions which can bedetermined routinely by one skilled in the art. To release the viralgenome, the particles are disrupted by suspending the pellets in analiquot of an SDS suspension, for example, one containing 1% SDS, 120 mMEDTA, 10 mM Tris-HCl, pH 7.5, which also contains 2 mg/ml proteinase K,which is followed by incubation at appropriate conditions, for example,45° C. for 90 minutes. Nucleic acids are isolated by adding, forexample, 0.8 μg MS2 bacteriophage RNA as carrier, and extracting themixture four times with a 1:1 mixture of phenol:chloroform (phenolsaturated with 0.5M Tris-HCl, pH 7.5, 0.1% (v/v) beta-mercaptoethanol,0.1% (w/v) hydroxyquinolone, followed by extraction two times withchloroform. The aqueous phase is concentrated with, for example,1-butanol prior to precipitation with 2.5 volumes of absolute ethanolovernight at −20° C. Nucleic acids are recovered by centrifugation in,for example, a Beckman SW41 rotor at 40,000 rpm for 90 min at 4° C., anddissolved in water that is treated with 0.05% (v/v) diethylpyrocarbonateand autoclaved.

Nucleic acid obtained by the above procedure is denatured with, forexample, 17.5 mM CH₃HgOH; cDNA then is synthesized using this denaturednucleic acid as template, and is cloned into the EcoRI site of phagelambda-gt11, for example, by using methods described by Huynh (1985)supra, except that random primers replace oligo(dT) 12-18 during thesynthesis of the first nucleic acid strand by reverse transcriptase (seeTaylor et al., [1976]). The resulting double stranded nucleic acidsequences are fractionated according to size on a Sepharose CL-4Bcolumn, for example. Eluted material of approximate mean size 400, 300,200 and 100 base-pairs are pooled into genomic pools. The lambda-gt11cDNA library is generated from the cDNA in at least one of the pools.Alternatively, if the etiological agent is a DNA virus, methods forcloning genomic DNA may be useful and are known to those skilled in theart.

The so-generated lambda-gt11 genomic library is screened for epitopesthat can bind specifically with serum, plasma or a liver homogenate froman individual who had previously experienced non-A, non-B, non-C, non-Ehepatitis (one which meets the criteria as set forth hereinbelow). About10⁴-10⁷ phage are screened with sera, plasma, or liver homogenates usingthe methods of Huyng et al. (supra). Bound human antibody can bedetected with sheep anti-human Ig antisera that is radio-labeled with¹²⁵I or other suitable reporter molecules including HRPO, alkalinephosphatase and others. Positive phage are identified and purified.These phage then are tested for specificity of binding to sera from apre-determined number of different humans previously infected with theHGBV agent, using the same method. Ideally, the phage will encode apolypeptide that reacts with all or a majority of the sera, plasma orliver homogenates that are tested, and will not react with sera, plasmaor liver homogenates from individuals who are determined to be“negative” according to the criteria set forth herein for the HGBV agentas well as hepatitis A, B, C, D and E. By following these procedures, aclone that encodes a polypeptide which is specifically recognizedimmunologically by sera, plasma or liver homogenates from non-A, non-B,non-C, non-D and non-E-identified patients can be isolated.

The present invention will now be described by way of examples, whichare meant to illustrate, but not to limit, the spirit and scope of theinvention.

EXAMPLES

The examples provided herein describe in detail methods which led to thediscovery of the HGBV group of viruses. The examples are provided inchronological order so that the discovery of the HGBV-A, HGBV-B andHGBV-C viruses of the HGBV group can be followed. Generally,transmissibility and infectivity studies were initially performed; thesestudies and subsequent ones described herein led to evidence for theexistence of two HCV-like viruses in HGBV: GB-A and GB-B. Subsequentexperiments also detailed herein utilizing degenerative primers led tothe discovery of HGBV-C. The prevalence of this group of viruses inhumans as evidenced by serological studies, the viral characterizationof this group of viruses, the relatedness of HGBV to other viruses inits proposed genus and the interrelatedness of HGBV-A, HGBV-B and HGBV-Calso is taught.

Example 1 Transmissibility of HGBV

A. Experimental Protocol. Sixteen tamarins (Saguinus labiatus) weresecured through LEMSIP (Laboratory for Experimental Medicine and Surgeryin Primates, Tuxedo, N.Y.) for the transmissibility and infectivitystudies. All animals were maintained and monitored at LEMSIP accordingto protocols approved by LEMSIP. (Note: one animal died of naturalcauses and one ailing animal was euthanized prior to the initiation ofinfectivity studies). Baseline serum liver enzyme values wereestablished for serum liver enzymes alanine transaminase (ALT),gamma-glutamyltransferase (GGT) and isocitric dehydrogenase (ICD) fortwo to three months on serum specimens obtained weekly or bi-weekly. Aminimum of eight serum liver enzyme values were obtained for each animalprior to inoculation. Cutoff values (CO) were determined for eachanimal, based on the mean liver enzyme value plus 3.75 times thestandard deviation. Liver enzyme values above the cutoff value wereinterpreted as abnormal and suggestive of liver damage. Several tamarinswere inoculated as described hereinbelow and monitored for changes inALT, GGT and ICD serum levels. At specified times thereafter during themonitoring process, certain animals were sacrified in order to obtainserum and tissues for further studies.

B. Inoculation of Animals (Initial Study). A pool of known infectioustamarin GB serum (passage 11, designated as H205 GB pass 11) wasprepared from serum collected during the early acute phase (19-24 dayspost inoculation) of hepatitis from nine tamarins inoculated with theHGBV. This pool had been previously described and studied in an effortto determine the etiological agent involved. J. L. Dienstag et al.,Nature 264 supra; E. Tabor et al., J. Med. Virol. 5, supra. Aliquots ofthis pool were maintained at Abbott Laboratories (North Chicago, Ill.60064) under liquid nitrogen storage conditions until utilized in thisstudy. Other aliqouts of HGBV are available from the American TypeCulture Collection (A.T.C.C.), 12301 Parklawn Drive, Rockville, Md.20852, under A.T.C.C. Deposit.No. VR-806.

On day one, four tamarins of the initial group of remaining 14 tamarins,identified as T-1053, T-1048, T-1057 and T-1061, were inoculatedintravenously with 0.25 ml of pool H205, passage 11, previously diluted1:50. These animals were monitored weekly for changes in the liverenzymes ALT, GGT and ICD. TABLE 2 presents the pre- and post-inoculationliver enzyme data on these four tamarins (T-1053, T-1048, T-1057 andT-1061); FIGS. 1-4 present the pre- and post-inoculation ALT and ICDlevels of these four tamarins. As the data demonstrate, significantrises in ALT, GGT and ICD above the CO were obtained in the fourtamarins inoculated with the 1:50 dilution of pool H205.

On the same day (day one), one tamarin (T-1047) was inoculatedintravenously with 0.25 ml of pooled normal tamarin serum and used as anegative control, and another tamarin (T-1042) was inoculatedintraveneously with 0.25 ml of pooled normal human serum and served asan additional negative control. FIGS. 5-6 and TABLE 3 present the pre-and post-inoculation ALT and ICD levels of the two control tamarins(T-1047 and T-1042). As the data demonstrate, no rise in ALT or ICD wasdocumented post-inoculation for the two control tamarins for a period ofeight weeks.

On the same day (day one), one tamarin (T-1044) was inoculatedintravenously with 0.2 ml of convalescent sera obtained from the surgeon(original GB source) approximately three weeks following the onset ofacute hepatitis. This specimen had been stored at −20° C. F. Deinhardtet al., J. Exper. Med. 125:673-688 (1967). Another tamarin (T-1034) wasinoculated with 0.1 ml of this convalescent sera. As FIGS. 7-8 and TABLE4 demonstrate, no rise in serum liver enzymes was observed in thesetamarins for a period of eleven weeks post inoculation. Thus, these datademonstrate that infective HGBV was not detectable in the convalescentsera obtained from the original patient and stored at −20° C., whichcould indicate that the individual had recovered from infection and thatthe virus had been cleared from the patient's serum or that the viraltiter had been reduced to non-detectable levels upon storage at −20° C.

C. Further Studies. Tamarin T-1053 showed a significant rise in serumliver enzymes one week post-inoculation, and was retested for liverenzymes on day 11 post-inoculation. At day 12 it was determined thatsignificant elevations in serum liver enzymes were present, and theanimal was sacrificed on that day. Plasma, liver and spleen tissuesamples were obtained for further studies. The plasma from T-1053 servedas the source for the RDA procedure discussed in Example 3 below; theliver tissue was utilized in Example 8 below.

Tamarins T-1048, T-1057 and T-1061 were monitored for serum liver enzymevalues; all were observed to exhibit elevated serum liver enzyme levelswithin two weeks following inoculation; these elevated values were notedfor six or more weeks post inoculation. All three tamarins were observedto have decreasing serum liver enzyme levels below the CO by 84 dayspost inoculation. On day 97 post inoculation, these three tamarins(T-1048, T-1057 and T-1061) were re-challenged with 0.10 ml of neatplasma obtained from tamarin T-1053 (shown to be infectious, see Example2) to determine whether hepatitis as documented by elevations in serumliver enzymes could be re-induced. The data are presented in TABLE 2 andFIGS. 1, 3 and 4. As the data indicates, serum liver enzyme levels oftwo tamarins (T-1057 and T-1061) remained below the CO for three weekspost reinoculation. One tamarin (T-1048) exhibited mild elevations inserum liver enzyme levels two weeks immediately post-reinoculation. Itwas hypothesized that the mild elevations in T-1048 were attributable toeither reinfection of liver tissue by HGBV or incomplete recovery fromthe initial inoculation with H205.

Example 2 Infectivity Studies

A. Experimental Protocol. Baseline readings on four tamarins wereobtained as described in Example 1(A). Briefly, baseline serum liverenzymes (ALT, GGT and ICD) were established for each animal prior toinoculation. Cutoff values (CO) were determined for each animal, basedon the mean liver enzyme value plus 3.75 times the standard deviation.Liver enzyme values above the cutoff were interpreted as abnormal andsuggestive of liver damage.

B. Inoculation of Tamarins. The plasma from Tamarin T-1053, sacrificedat day 12 post inoculation (see Example 1[C]), was used as the inoculumfor further studies. On day one, one tamarin (T-1055) was inoculatedintravenously with 0.25 ml of neat T-1053 plasma. On the same day, twotamarins (T-1038 and T-1051) were inoculated intravenously with 0.25 mlof T-1053 plasma which had been serially diluted to either 10⁻⁴ (T-1038)or 10⁻⁵ (T-1051) in pooled normal tamarin plasma. On the same day,tamarin T-1049 was inoculated intravenously with 0.25 ml of plasmaT-1053 which had been filtered through a series of filters of decreasingpore size (0.8 μm, 0.45 μm, 0.22 μm and 0.10 μm) and diluted at 10⁻⁴ inpooled normal tamarin plasma.

All tamarins (T-1055, T-1038, T-1051 and T-1049) were monitored weeklyas described in Example 1 for changes in serum liver enzymes ALT, GGTand ICD. TABLE 5 presents the pre- and post-inoculation liver enzymedata on these four tamarins. FIG. 9 presents the pre- andpost-inoculation ALT and ICD values T-1055. Referring to FIG. 9, it canbe seen that elevations above the CO in serum liver enzymes ALT and ICDoccurred. This tamarin was sacrified on day 12 post-inoculation. FIGS.10 and 11 present the pre- and post-inoculation serum levels of ALT andICD for tamarins T-1051 and T-1038, respectively. Referring to FIGS. 10and 11, it can be seen that elevations in serum liver enzymes ALT andICD occured in both animals by 11 days post-inoculation. T-1038 wassacrified on day 14 post inoculation. TABLE 5 and FIG. 12 present thedata obtained on T-1049. As can be seen from TABLE 5 and FIG. 12,elevations in serum liver enzymes above the CO were observed in T-1049within 11 days post-inoculation.

The filtration study conducted on T-1049 indicates that HGBV can passthrough a 0.10 μm filter, thereby suggesting that HGBV is likely to beviral in nature, and less than 0.1 μm in diameter. In addition, theinfectivity titration experiment conducted on T-1038 demonstrates thatthe T 1053 serum contains at least 4×10⁵ tamarin infectious doses perml.

In order to show the transmissibility of a single HGBV agent, tamarinT-1044 was inoculated with 0.25 ml of an inoculum consisting of T-1057serum that had been obtained 7 days after the H205 inoculation anddiluted 1:500 in normal tamarin serum. Mild elevations in ALT levelsabove the cutoff were observed from days 14-63 PI (that it, elevationsin the range of 82 to 106).

Tamarins T-1047 and T-1056 were subsequently inoculated with 0.25 ml ofT-1044 serum obtained 14 days PI and diluted 1:2 in normal tamarinserum. Elevations in ALT levels above the cutoff were first observed inT-1047 and T-1056 at 42 days PI and returned to normal levels at days 64and 91 PI, respectively. Tamarin T-1058 was inoculated with 0.25 ml ofneat T-1057 serum obtained 22 days after the challenge with T-1053serum. Elevations in ALT levels have not been observed for 112 days PI.

Example 3 Representational Difference Analysis (SubtractiveHybridization)

A. Generation of Double-stranded DNA for Amplicons

Using the procedure described herein in Materials and Methods above andreferring to FIG. 13, tester amplicon was prepared from total nucleicacid obtained from tamarin T-1053 infectious plasma on day 12 postinoculation with H205 serum (see Examples 1C and 2B). Driver ampliconwas prepared from Tamarin T-1053 pre-inoculation plasma pooled from days−17 to −30 (see Example 1A). Briefly, both plasmas were filtered througha 0.1 μm filter as described in Example 2B. Next, 50 μl of each filteredplasma was extracted using a commercially available kit [United StatesBiochemical (USB), Cleveland, Ohio, cat. #73750] and 10 μg yeast tRNA asa carrier. This nucleic acid was subjected to random primed reversetranscription followed by random primed DNA synthesis using commerciallyavailable kits. Briefly, an 80 μl reverse transcription reaction wasperformed using Perkin Elmer's (Norwalk, Conn.) RNA PCR kit (cat. #N808-0017) as directed by the manufacturer using random hexamers andincubating for 10 minutes at 20° C. followed by 2 hours incubation at42° C. The reactions then were terminated and cDNA/RNA duplexesdenatured by incubation at 99° C. for 2 minutes. The reactions weresupplemented with 10 μl 10×RP buffer [100 mM NaCl, 420 mM Tris (pH 8.0),50 mM DTT, 100 μg/ml BSA], 250 pmoles random hexamers and 13 unitsSequenase® version 2.0 polymerase (USB, cat. #70775) in a total volumeof 20 μl. The reactions were incubated at 20° C. for 10 minutes followedby 37° C. for 2 hours. After phenol:chloroform extraction and ethanolprecipitation, the double stranded DNA products of these reactions weredigested with 4 units of restriction endonuclease Sau3A I (New EnglandBiolabs [NEB], cat. #169L) in 30 μl reaction volumes for 30 minutes, asdirected by the supplier.

B. Generation of Amplicons

Sau3AI-digested DNA was extracted and precipitated as described above.The entire Sau3AI-digested product was annealed to 465 pmoles R Bgl 24(SEQUENCE I.D. NO. 1) and 465 pmoles R Bgl 12 (SEQUENCE I.D. NO. 2) in a30 μl reaction volume buffered with 1×T4 DNA ligase buffer (NEB) byplacing the reaction in a 50-55° C. dry heat block which was thenincubated at 4° C. for 1 hour. The annealed product was ligated byadding 400 units T4 DNA ligase (NEB, cat. # 202S). After incubation for14 hours at 16° C., a small scale PCR was performed. Briefly, 10 μl ofthe ligation reaction was added to 60 μl H₂O, 20 μl 5×PCR buffer (335 mMTris, pH 8.8, 80 mM [NH₄]₂SO₄, 20 mM MgCl₂, 0.5 μg/ml bovine serumalbumin, and 50 mM 2-mercaptoethanol), 8 μl of 4 mM dNTP stock, 2 μl(124 pmoles) R Bgl 24 (SEQUENCE I.D. NO. 3) and 3.75 units of AmpliTaq®DNA polymerase (Perkin Elmer, cat. # N808-1012). The PCR amplificationwas performed in a GeneAmp® 9600 thermocycler (Perkin Elmer). Sampleswere incubated for 5 min. at 72° C. to fill-in the 5′-protruding ends ofthe ligated adaptors. The samples were amplified for 25 to 30 cycles (1min. at 95° C. and 3 min. at 72° C.) followed by extension of 72° C. for10 min. After agarose gel confirmation of successful amplicon generation(ie. a smear of PCR products ranging from approximately 100 bp to over1500 bp), a large scale amplification of tester and driver amplicons wasperformed. Forty 100 μl PCRs and eight 100 μl PCRs were set up asdescribed above for the prepartion of driver and tester amplicons,respectively. Two μl from the small scale PCR product per 100 μlreaction served as the template for the large scale amplicon generation.Thermocycling was performed as described above for an additional 15 to20 cycles of amplification. The PCR reactions for both driver and testerDNA were then phenol/chloroform extracted twice, isopropanolprecipitated, washed with 70% ethanol and digested with Sau3AI to cleaveaway the adaptors. The tester amplicon was further purified on a lowmelting point agarose gel. Briefly, 10 μg of tester amplicon DNA was runon a 2% SeaPlaque® gel (FMC Bioproducts, Rockland, Me.). Fragments of150-1500 base pairs were excised from the gel, the gel slice was meltedat 72° C. for 20 minutes with 3 ml H₂O, 400 μl 0.5 M MOPS and 400 μlNaCl. DNA was recovered from the melted gel slice using a Qiagen-tip 20(Qiagen, Inc., Chatsworth, Calif.) as directed by the manufacturer.

C. Hybridization and Selective Amplification of Amplicons

Approximately 2 μg of purified tester DNA amplicon was ligated to N Bgl24 (SEQUENCE I.D. NO.3) and N Bgl 12 (SEQUENCE I.D. NO. 4) as describedabove. For the first subtractive hybridization, tester amplicon ligatedto the N Bgl primer set (0.5 μg) and driver amplicon (20 μg) were mixed,phenol/chloroform extracted and ethanol precipitated. The DNA wasresuspended in 4 μl of EE×3 buffer (30 mM EPPS, pH 8.0 at 20° C. [Sigma,St. Loius, Mo.], 3 mM EDTA) and overlaid with 35 μl of mineral oil.Following heat denaturation (3 min at 99° C.), 1 μl of 5 M NaCl wasadded to the denatured DNA and the DNA was allowed to hybridize at 67°C. for 20 hours. The aqueous phase was removed to a new tube and 8 μl oftRNA (5 mg/ml) was added to the sample followed by 390 μl TE (10 mMTris, pH 8.0 and 1 mM EDTA). Eighty μl of the hybridized DNA solutionwas added to 480 μl H₂O, 160 μl 5×PCR buffer (above), 64 μl 4 mM dNTPsand 6 μl (30 units) AmpliTaq® polymerase. This solution was incubated at72° C. for 5 min. to fill in the 5′ overhangs created by the ligated NBgl 24 primer. N Bgl 24 (SEQUENCE I.D. NO. 3, 1.24 nmoles in 20 μl H₂O)was added, the reaction was aliquoted (100 μl/tube) and subjected to 10cycles of amplification as described above. The reaction was pooled,phenol/chloroform extracted twice, isopropanol precipitated, washed with70% ethanol and resuspended in 40 μl H₂O. Single-stranded DNA wasremoved by mung bean nuclease (MBN). Briefly, 20 μl amplified DNA wasdigested with 20 units MBN (NEB) in a 40 μl reaction as described by thesupplier. One hundred and sixty μl 50 mM Tris, pH 8.8 was added to theMBN digest. The enzyme was heat inactivated at 99° C. for 5 min. Eightyμl of the MBN-digested DNA was PCR amplified as described above for anadditional 15 cycles. Again, the reaction was pooled, phenol/chloroformextracted twice, isopropanol precipitated, washed with 70% ethanol andresuspended in H₂O. The amplified DNA (3 to 5 μg) was then digested withSau3A I, extracted and precipitated as described above. The final DNApellet was resuspended in 100 μl TE.

D. Subsequent Hybridization/Amplification Steps

One hundred ng of the DNA from the previous hybridization/selectiveamplification was ligated to the J Bgl primer set (SEQUENCE I.D. NO. 5and SEQUENCE I.D. NO. 6) as described previously. This DNA (50 ng) wasmixed with 20 μg of driver amplicon and the hybridization andamplificiation procedures were repeated as described above except thatthe extention temperature during the thremocycling was 70° C. and not72° C. as for the N Bgl primer set (SEQUENCE I.D. NO. 3 and SEQUENCEI.D. NO. 4) and the final amplification step (after MBN digestion) wasfor 25 cycles. One hundred ng of the second hybridization-amplificationproduct was then ligated to the N Bgl primer set (SEQUENCE I.D. NO. 3and SEQUENCE I.D. NO. 4), and 200 pg of this material together with 20μg of driver amplicon was taken for the third round ofhybridization/amplification as described above with the finalamplification for 25 cycles.

A 2% agarose gel of the products from the representational differenceanalysis (RDA) performed on pre-HGBV inoculated and acute phase T-1053plasma is shown in FIG. 14. Referring to FIG. 14, Lane 1 contains 150 ngof HaeIII digested Phi-X174 DNA marker (NEB) with the appropriate size(in bp) of the DNA fragments. The complexity of the driver amplicon(lane 2) and the tester amplicon (lane 3) is evidenced by the smear ofDNA products seen in these samples. This complexity drops dramaticallyas the tester sequences are subjected to one (lane 4), two (lane 5) orthree (lane 6) rounds of hybridization/selective amplification.

E. Cloning of the Difference Products

The difference products were cloned into the BamHI site of pBluescriptII KS+ (Stratagene, La Jolla, Calif., cat. # 212207), as follows.Briefly, 0.5 μg pBluescript II was digested with BamHI (10 units, NEB)and 5′ dephosphorylated with calf intestinal phosphatase (10 units, NEB)as directed by the supplier. The plasmid was phenol:chloroformextracted, ethanol precipitated, washed with 70% ethanol and resuspendedin 10 μl H₂O (final concentration approximately 50 ng pBluescript II perμl). The four largest bands from the second hybridization/amplificationproducts were excised from a 2% low melting point agarose gel asdescribed above. Four μl of the melted (72° C., 5 min.) gel slices wereligated to 50 ng of the BamHI-cut, dephosphorylated pBluescript II in a50 μl reaction using the Takara DNA ligation kit (Takara Biochemical,Berkeley, Calif.). After incubating at 16° C. for 3.5 hours, 8 μl of theligation reactions were used to transform E. coli competent XL-1 Bluecells (Stratagene) as directed by the supplier. The transformationmixtures were plated on LB plates supplemented with ampicllin (150μg/ml) and incubated overnight at 37° C. The resulting colonies weregrown up in liquid culture and miniprep plasmid DNA was analyzed asdescribed in the art to confirm the existence of cloned product.

In addition to the cloning of the four largest products from the secondhybridization/amplification step, the entire population of products fromthe third hybridization/amplification step was cloned into pBluescriptII. Briefly, 50 ng pBluescript II vector (prepared as above) was ligatedto 10 ng of the third hybridization/amplification products in a 50 μlreaction as described above. After incubation at 16° C. for 2 hours, 10μl ligation product was used to transform E. coli competent XL-1 Bluecells as before. Sixty colonies from the resultant transformation weregrown up, and miniprep DNA was prepared and analyzed as described andknown in the art. Restriction endonuclease digestion and dot blothybridization experiments were used to identify unique clones.

Example 4 Imunoisolation of a cDNA Clone Encoding an Antigenic Region ofthe HGBV Genome

A. Preparation of Concentrated Virus as a Source of Cloning Material

The following isolation scheme was employed to isolate the HGBV genomein addition to the procedures exemplified in Example 3. Three tamarins(T-1055, T-1038 and T-1049) were inoculated with serum prepared fromtamarin T-1053 as described in Example 2. Referring to TABLE 5, elevatedliver enzyme values were noted in all 3 tamarins by day 11 PI. TamarinT-1055 was sacrificed on day 12 PI and tamarins T-1038 and T-1049 weresacrificed on day 14 PI. Approximately 3-4 ml of serum from each ofthese three tamarins were pooled, providing a total volume ofapproximately 11.3 ml. The pooled serum was clarified by centrifugationat 10,000×g for 15 min at 15° C. It was then passed successively through0.8, 0.45, 0.2, and 0.1 μm syringe filters. This filtered material wasthen concentrated by centrifugation through a 0.3 ml CsCl cushion(density 1.6 g/ml, in 10 mM Tris, 150 mM NaCl, 1 mM EDTA, pH 8.0) in aSW41-Ti rotor at 41,000 rpm at 4° C. for 68 min. The CsCl layer,approximately 0.6 ml, was removed following centrifigation and stored inthree 0.2 ml aliquots at −70° C.

Tamarin T-1034 was subsequently inoculated with 0.25 ml of a 10⁻⁶dilution of this pelleted material (prepared in normal tamarin serum).Elevated ALT liver enzyme values were first noted in T-1034 at 2 weeksPI, and remained elevated for the next 7 weeks, finally normalizing byweek 10 PI (see FIG. 30, Example 14). This experiment demonstrated theinfectivity of the material concentrated from the pooled tamarin sera.Since this material was shown to be of a relatively high titer, thisconcentrated source of virus was used as the source of nucleic acid forthe preparation of a cDNA library, as described below.

B. cDNA Library Construction

An aliquot (0.2 ml) of the concentrated virus (described above) wasextracted for RNA using a commercially available RNA extraction kit(Stratagene, La Jolla, Calif.) as instructed by the supplier. The samplewas divided into four equal aliquots prior to the final precipitationstep, and then precipitated in the presence of 5 μg/ml yeast tRNA. Onlyone of these aliquots was used for cDNA synthesis; the others werestored at −80° C. Phosphorylated, blunt-ended, double-stranded cDNA wasprepared from the RNA using a commercially available kit (Stratagene, LaJolla, Calif.) as directed by the manufacturer. A double-strandedlinker/primer was then ligated to the cDNA ends (sense strand, SEQUENCEI.D. NO. 7; antisense strand, SEQUENCE I.D. NO. 8) in a 10 μl reactionvolume using a T4 DNA ligase kit (Stratagene, La Jolla, Calif.) asdirected by the manufacturer. This provided all cDNAs in the mixturewith identical 5′ and 3′ ends containing Not I and Eco RI restrictionenzyme recognition sites. G. Reyes and J. Kim, Mol. Cell. Probes5:473-481 (1991); A. Akowitz and L. Manuelidis, Gene 81:295-306 (1989);and G. Inchauspe et al., in Viral Hepatitis and Liver Disease, F. B.Hollinger et al., Eds., pp. 382-387 (1991). The sense-strandoligonucleotide of the linker/primer was then used as a primer in a PCRreaction such that all cDNAs were amplified independent of theirsequence. This procedure allowed for the amplification of rare cDNAspresent within the total cDNA population to a level which allowed themto be efficiently cloned, thus producing a cDNA library that isrepresentative of the sequences within the starting material.

PCR was performed on a 1 μl aliquot of the above ligate in the presenceof the sense-strand oligonucleotide primer (final concentration: 1 μM;reaction volume: 50 μl) using the GeneAmp PCR kit (Perkin-Elmer) asdirected by the manufacturer in a PE-9600 thermocycler. Thirty cycles ofPCR were performed as follows: denaturation at 94° C. for 0.5 min,annealing at 55° C. for 0.5 min, and extension at 72° C. for 1.5 min. A1 μl aliquot of the resulting products was then re-amplified asdescribed above. The final PCR reaction products were then extractedonce with an equal volume of phenol-chloroform (1:1, v/v) and once withan equal volume of chloroform, and then precipitated on dry ice for 10min following the addition of sodium acetate (final concentration, 0.3M) and 2.5 volumes of absolute ethanol. The resulting DNA pellet wasresuspended in water and digested with the restriction enzyme Eco RI(New England Biolabs) as directed by the manufacturer. The digestedcDNAs were then purified from the reaction mixture using a DNA bindingresin (Prep-a-Gene, BioRad Laboratories) as directed by the manufacturerand eluted in 20 μl of distilled water.

The cDNAs (8 μl) were ligated to 3 μg lambda gt11 vector DNA arms(Stratagene, La Jolla, Calif.) in a reaction volume of 30 μl at 4° C.for 1-5 days. Eleven microliters of the ligate was packaged into phageheads using GigaPack III Gold packaging extract (Stratagene, La Jolla,Calif.) as directed by the manufacturer. The resulting library containeda total of approximately 1.73 million members (PFU) at a recombinationfrequency of 89.3% with an average insert size of approximately 350 basepairs.

C. Immunoscreening of the Recombinant GB cDNA Library

The antiserum used for immunoscreening of the cDNA library was obtainedfrom tamarins that had demonstrated elevations in their serum liverenzyme levels following inoculation. Two separate pools of antisera wereused for immunoscreening. The first pool contained serum from twoanimals (T-1048 and T-1051; see Example 1, TABLE 2, and Example 2, TABLE5, respectively) while the second pool contained serum from a singleanimal (T1034; see FIG. 30, Example 14). The specific sera used areshown in TABLE 6.

At the time that these samples were chosen for use in cDNA libraryimmunoscreening, they had not been tested for their immunoreactivitywith either the 1.4 or 1.7 recombinant CKS proteins (Example 13).Therefore, the results shown herein were obtained independent of anyinformation regarding the presence or absence of HGBV antibodies againstthese recombinant proteins within the antiserum used.

TABLE 6 Tamarin Sera used for Immunoscreening of GB cDNA Library TamarinTamarin Tamarin 1048^(a) 1051^(b) 1034^(c) Days Post- Volume in DaysPost- Volume in Days Post- Volume in Inoculate Pool Inoculate PoolInoculate Pool 63 0.2 ml 63 0.2 ml 42 0.1 ml 77 0.2 ml 69 0.1 ml 49 0.1ml 91 0.2 ml 91 0.2 ml 63 0.1 ml 97 0.2 ml 98 0.2 ml 70 0.1 ml 126  2.0ml 105  0.2 ml 77 0.08 ml  109  5.3 ml ^(a)Total T-1048 pool volume is2.8 ml. ^(b)Total T-1051 pool volume is 6.4 ml. One ml of each pool wassaved and the remainder of each was combined and used as the primaryantiserum for immunoscreening. ^(c)Total T-1034 pool volume is 0.48 ml;the entire pool was used for immunoscreening.

The procedure used for the immunoisolation of recombinant phage wasbased upon the method described by Young and Davis with modifications asdescribed below. R. A. Young and R. W. Davis, PNAS 80:1194-1198 (1983).Two immunoscreening experiments were performed, one utilizing antiserumpooled from T-1048 and T-1051 and the other utilizing antiserum fromT-1034. In both cases, the primary antiserum was pre-adsorbed against E.coli extract prior to use in order reduce non-specific interactions ofantibody with E. coli proteins. In the first experiment, 1.29 millionrecombinant phage were immunoscreened with the T-1048/T-1051 antiserumpool; in the second experiment 0.30 million recombinant phage wereimmunoscreened with T-1034 antiserum. The recombinant phage library wasplated on a lawn of E. coli strain Y1090r- and grown at 37° C. for 3.5hours. The plates were then overlayed with nylon filters that weresaturated with IPTG (10 mM) and the plates incubated at 42° C. for 3.5hours. The filters were then blocked in Tris-saline buffer containing 1%BSA, 1% gelatin, and 3% Tween-20 (“blocking buffer”) for 1 hour at 22°C. The filters were then incubated in primary antiserum (1:100 dilutionin blocking buffer) at 4° C. for 16 hours. Primary antiserum was thenremoved and saved for subsequent rounds of plaque purification, and thefilters washed four times in Tris-saline containing 0.1% Tween-20. Thefilters were then incubated in blocking buffer containing 125-I-labeled(or alkaline-phosphatase conjugated) goat anti-human IgG (available fromJackson ImmunoResearch, West Grove, Pa.) for 60 min at 22° C., washed asdescribed above, and then exposed to x-ray film (or subjected to colordevelopment according to established procedures, as in J. Sambrook etal., Molecular Cloning: A Laboratory Manual, 2nd edition, Cold SpringHarbor Press, Cold Spring Harbor, N.Y., 1989). Five immunopositive phage(4-3B1, 48-1A1, 66-3A1, 70-3A1, 78-1C1) were isolated from this libraryand subsequently tested for specificity of binding to antisera fromthree infected tamarins (T-1048, T-1051, T-1034) using the methoddescribed above. These recombinants encoded polypeptides that reactedwith convalescent sera, but not with pre-inoculation sera, from each ofthe three infected tamarins (data not shown).

In order to verify the specificity of the immunological reactivity ofthe polypeptide encoded by the recombinant phage, each cDNA was rescuedfrom the lambda phage genome by PCR using primers located 5′ (SEQUENCEI.D. NO. 9) and 3′ (SEQUENCE I.D. NO. 10) to the Eco RI cloning site.The PCR products were then digested with Eco RI and subsequently ligatedinto the E. coli expression plasmid pJO201 as described in Example 13.Insertion of the cDNAs into the Eco RI site of pJO201 maintained thetranslational reading frame of this cDNA as present in the lambda phageclone. The subclones in the pJO201 expression vector were designated4-3B1.1, 48-1A1.1, 66-3A1.49, 70-3A1.37, and 78-1C1.17. Immunoblotanalysis (as in Example 13) of E. coli lysates prepared from culturesexpressing these cDNAs with convalescent sera from tamarins T-1034,T-1048, and T-1051 (1:100 dilution) demonstrated specific immunologicreactivity with a protein of the size predicted for each CKS-fusionprotein. (data not shown). The DNA sequence of each of the cDNAs wasdetermined and it was found that these clones possessed nearly 100%sequence identity with that of HGBV-B virus (SEQUENCE I.D. NO. 11). Thesequence of the 4-3B1.1 insert (SEQUENCE I.D. NOS. 12 and 13), althoughnot determined in its entirety, those portions that have been sequencedexhibit 99.5% Sequence identity to a portion of the sequence withinHGBV-B (SEQUENCE I.D. NO. 11) from base pairs 6834-7458. This region ofthe HGBV-B (SEQUENCE I.D. NO. 11) sequence showing identity with that ofthe sequence obtained from clone 4-3B1.1 was translated into the C.1reading frame and is presented in the sequence listing as SEQUENCE I.D.NO. 14. The sequence of the 48-1A1.1 insert (SEQUENCE I.D. NO. 15)exhibits 100% Sequence identity to a portion of the sequence from HGBV-B(SEQUENCE I.D. NO. 11, see Example 9) from base pairs 4523-4752. The DNAsequence corresponding to SEQUENCE I.D. NO. 15 was translated into the+1 reading frame and is presented in the sequence listing as SEQUENCEI.D. NO. 16. The sequence of the 66-3A1.49 insert (SEQUENCE I.D. NO. 17)exhibits essentially 100% sequence identity to that of clone 48-1A1.1and thus no protein translation is shown in the sequence listing. Thesequence of the 70-3A1.37 insert (SEQUENCE I.D. NO. 18) exhibits 100%sequence identity to a portion of the sequence from HGBV-B (SEQUENCEI.D. NO. 11) from base pairs 6450-6732 except for a three base-pairdeletion corresponding to bases 6630-6632 of the HGBV-B sequence(SEQUENCE I.D. NO. 11). The DNA sequence corresponding to SEQUENCE I.D.NO. 18 was translated into the +2 reading frame and is presented in thesequence listing as SEQUENCE I.D. NO. 19. The sequence of the 78-1C1.17insert (SEQUENCE I.D. NO. 20) exhibits 100% sequence identity to that ofclone 70-3A1.37 and thus no protein translation is shown in the sequencelisting. These data demonstrate that the cDNA clones isolated from thelambda gt11 cDNA library are derived from the genome of the HGBV agentand that it encodes polypeptides which are specifically recognizedimmunologically by sera from GB-infected tamarins. Clones48-1A1.1(“clone 48”) 4-3B1.1, 66-3A1.49, 70-3A1.37, and 78-1C1.17 havebeen deposited at the American Type Culture Collection as providedhereinabove.

Example 5 DNA Sequence Analysis of HGBV Clones

Unique clones obtained in Example 3 were sequenced using thedideoxynucleotide chain termination technique (Sanger, et al., supra) ina kit form (Sequenase® version 2.0, USB). These sequences arenon-overlapping and are presented in the Sequence Listing as clone 4(SEQUENCE I.D. NO. 21), clone 2 (SEQUENCE I.D. NO. 22), clone 10(SEQUENCE I.D. NO. 23), clone 11 (SEQUENCE I.D. NO. 24), clone 13(SEQUENCE I.D. NO. 25), clone 16 (SEQUENCE I.D. NO. 26), clone 18(SEQUENCE I.D. NO. 27), clone 23 (SEQUENCE I.D. NO. 28), clone 50(SEQUENCE I.D. NO. 29) and clone 119 (SEQUENCE I.D. No. 30). Clones 4,2, 10, 11, 13, 16, 18, 23, 50 and 119 have been deposited at theA.T.C.C. Clone 2 was accorded A.T.C.C. Deposit No. 69556; Clone 4 wasaccorded A.T.C.C. Deposit No. 69557; Clone 10 was accorded A.T.C.C.Deposit No. 69558; Clone 16 was accorded A.T.C.C. Deposit No.69559;Clone 18 was accorded A.T.C.C. Deposit No. 69560; Clone 23 was accordedA.T.C.C. Deposit No. 69561; and Clone 50 was accorded A.T.C.C. DepositNo. 69562; Clone 11 was accorded A.T.C.C. Deposit No. No. 69613; Clone13 was accorded A.T.C.C. Deposit No. 69611; and Clone 119 was accordedA.T.C.C. Deposit No. 69612.

The sequences were searched against the GenBank database using theBLASTN algorithm (Altschul et al, J. Mol. Biol. 215:403-410 [1990]).None of these sequences were found in GenBank, indicating that thesesequences have not been previously characterized in the literature. TheDNA sequences were translated into the six possible reading frames andare presented in the sequence listing (SEQUENCE I.D. NO. 21 translatesto SEQUENCE I.D. NOS.31-36, SEQUENCE I.D. NO. 22 translates to SEQUENCEI.D. NOS. 37-42, SEQUENCE I.D. NO. 23 translates to SEQUENCE I.D. NOS.43-48, SEQUENCE I.D. NO. 26 translates to SEQUENCE I.D. NOS. 49-54,SEQUENCE I.D. NO. 27 translates to SEQUENCE I.D. NOS. 55-60, SEQUENCEI.D. NO. 28 translates to SEQUENCE I.D. NOS. 61-66, and SEQUENCE I.D.NO. 29 translates to SEQUENCE I.D. NOS. 67-72). SEQUENCE I.D. NO. 24 iscontained within SEQUENCE I.D. NO. 73 (described in Example 9), whichtranslates to SEQUENCE I.D. NOS. 74-79. SEQUENCE I.D. NOS. 25 and 30 arecontained within SEQUENCE I.D. NO. 80 (described in Example 9), whichtranslates to SEQUENCE I.D. NO. 81-86. The translated sequences wereused to search the SWISS-PROT database using the BLASTX algorithm (Gishet al., Nature Genetics 3:266-272 [1993]). Again, none of thesesequences were found in SWISS-PROT indicating that these sequences havenot been previously characterized in the literature.

Homology searches conducted using the BLASTN, BLASTX and FASTdbalgorithms demonstrate some, albeit low, sequence resemblence tohepatitis C virus (TABLE 7, below). Specifically, translations of clones4 (SEQUENCE I.D. NO. 35), 10 (SEQUENCE I.D. NO. 44), 11 (residues 1-166of GB-A, frame 3 [SEQUENCE I.D. NO. 76]), 16 (SEQUENCE I.D. NO. 50), 23(SEQUENCE I.D. NO. 65), 50 (SEQUENCE I.D. NOS. 70 and 72) and 119(residues 912-988 of GB-A, frame 3 [SEQUENCE I.D. NO. 83]), are between24.1% and 45.1% homlogous to various HCV isolates at the amino acidlevel. Of particular interest, translation of clone 10 (SEQUENCE I.D.NO. 44) showed limited homology to the putative RNA-dependent RNApolymerase of HCV. A comparison of the conserved amino acids present inthe putative RNA-dependent RNA polymerase of other positive strandviruses (Jiang et al. PNAS 90:10539-10543 [1993]) with the putativeamino acid translation of clone 10 (SEQUENCE I.D. NO. 44) revealed thatconserved amino acid residues of other RNA-dependent RNA polymerases arealso conserved in clone 10 (SEQUENCE I.D. NO. 44). This includes thecanonical GDD (Gly-Asp-Asp) signature sequence of RNA-dependent RNApolymerases. Thus, clone 10 (SEQUENCE I.D. NO. 44) appears to encode aviral RNA-dependent RNA polymerase. Surprisingly, only clone 10(SEQUENCE I.D. NO. 44) showed any sequence homology with HCV at thenucleotide level when the BLASTN algorithm was used. Clones 4 (SEQUENCEI.D. NO. 21), 16 (SEQUENCE I.D. NO. 26), 23 (SEQUENCE I.D. NO.28) and 50(SEQUENCE I.D. NO. 29) and 119 (SEQUENCE ID. NO. 30) which have low HCVhomology at the amino acid level, were not detected by BLASTN insearches of GenBank. In addition, clones 2 (SEQUENCE I.D. NOS. 37-42),13 (SEQUENCE I.D. NO. 25 and 37-42) and 18 (SEQUENCE I.D. NOS. 27 and55-60) showed no significant nucleotide or amino acid homology to HCVwhen searched against GenBank or SWISS-PROT as described hereinabove.

TABLE 7 HCV Homology of HGBV Cones Homology Clone Nucleotide^(a) AminoAcid^(b) Strain^(c) Region^(d) Function^(e)  4 none  28/73 (38.4%) HCVTWNS4 unknown 10 134/307 46/102 (45.1%) HCVJ6 NS5 replicase (43.6%)^(f) 11none 40/166 (24.1%) HCVJT NS5 replicase 16 none 55/177 (31.1%) HCVJ8NS2/3 protease 23 none 44/121 (36.4%) HCVJA NS3 helicase 50 none 29/112(25.9%) HCVH NS4/5 unknown 119  none  27/77 (35.1%) HCVTW NS5 replicase^(a)Homology found to HCV when GB clones were searched against GenBankusing the BLAST algorithm. ^(b)Homology found to HCV when translated GBclone sequences were searched against SWISS-PROT using the FASTdbalgorithm. ^(c)Most homologous strain of HCV (SWISS-PROT designation)^(d,e)Region of homology and reputed function of clone compared with HCVaccording to Houghton et al., Hepatology 14(2):381-388 (1991).^(f)BLASTN detected a segment of clone 10 that was 64% homologous withHCV NS5 over 132 nucleotides. Alignment of the entire clone 10 sequenceswith the homologous nucleotide sequence of HCVJ6 shows 43.6% homology.

Example 6 Exogenicity of HGBV Clones

The HGBV clones were not detected in normal or HGBV-infected tamarinliver DNA, normal human lymphocyte DNA, yeast DNA or E. coli DNA. Thiswas demonstrated for HGBV clones 2 (SEQUENCE I.D. NO. 22) and 16(SEQUENCE I.D. NO. 26) by Southern blot analysis. In addition, all HGBVclones were analyzed by genomic PCR to confirm the exogenous origin ofthe HGBV sequences with respect to the tamarin, human, yeast and E. coligenomes. These data are consistent with the viral nature of the HGBVsequences described in Example 5.

A. Southern Blot Analysis

Tamarin liver nuclei were obtained from low speed pelleting of liverhomogenates of HGBV-infected and normal tamarins (describedhereinbelow). DNA was extracted from nuclei using a commerciallyavailable kit (USB cat. # 73750) as directed by the supplier. Thetamarin DNA was treated with RNase during the extraction procedure.Human placental DNA (Clontech, Palo Alto, Calif.), yeast DNA(Saccharomyces cerevisiae, Clontech) and E. coli DNA (Sigma) wereobtained from commercial sources.

Each DNA sample was digested with BamHI (NEB) according to the suppliersdirection. Digested DNAs (10 μg) and RDA products (0.5 μg each fromExample 3B) were electrophoresed on 1% agarose gels and capillaryblotted to Hybond-N+ nylon membranes (Amersham, Arlington Heights, Ill.)as described in Sambrook et al. (pp. 9.34 ff). DNA was fixed to themembrane by alkali treatment as directed by the membrane supplier.Membranes were prehybridized in Rapid Hyb solution (Amersham) at 65° C.for 30 min.

Radiolabeled probes of the HGBV sequences were prepared by PCR. Briefly,50 μl PCRs were set up using 1×PCR buffer II (Perkin Elmer), 2 mM MgCl₂,20 μM dNTPs, 1 μM each of clone specific sense and antisense primers(for clone 2, SEQUENCE I.D. NOS. 87 and 88; for clone 4, SEQUENCE I.D.NOS. 89 and 90; for clone 10, SEQUENCE I.D. NOS. 91 and 92; for clone16, SEQUENCE I.D. NOS. 93 and 94; for clone 18, SEQUENCE I.D. NOS. 95and 96; for clone 23, SEQUENCE I.D. NOS. 97 and 98; and for clone 50,SEQUENCE I.D. NOS. 99 and 100), 1 ng HGBV clone plasmid (described inExample 3[E]), 60 μCi α-³²P-dATP (3000 Ci/mmol) and 1.25 units ofAmpliTaq® polymerase (Perkin Elmer). The reactions were incubated at 94°C. for 30 sec., 55° C. for 30 sec., and 72° C. for 30 sec. for a totalof 30 cycles of amplification followed by a final extension at 72° C.for 3 minutes. Unincorporated label was removed by Quick-Spin® G-50 spincolumns (Boehringer Mannheim, Indianapolis, Ind.) as directed by thesupplier. The probes were denatured (99° C., 2 min.) prior to additionto the pre-hybridized membranes.

Radiolabeled probes were added to the prehybridized membranes (2×10⁶dpm/ml) and filters were hybridized at 65° C. for 2.5 hours as directedby the Rapid Hyb® supplier. The hybridized membranes were washed underconditions of moderate stringency (1×SSC, 0.1% SDS at 65° C.) beforebeing exposed to autoradiographic film for 72 hours at −80° C. with anintensifying screen. These conditions were designed to detect a singlecopy gene with a similar radiolabeled probe.

The results show that clone 2 (SEQUENCE I.D. NO. 22) and clone 16(SEQUENCE I.D. NO. 26) sequences did not hybridize to DNA from normal orHGBV-infected tamarin liver (FIGS. 15 and 16, lanes 1B and 3B,respectively), human DNA (FIGS. 15 and 16, lane 1A), yeast DNA (FIGS. 15and 16, lane 2A) or E. coli DNA (FIGS. 15 and 16, lane 3A). In addition,no hybridization was detected with the driver amplicon DNA (FIGS. 15 and16, lanes 4A, derived from pre-HGBV-inoculated tamarin plasma asdescribed in Example 2.B). In contrast, strong hybridization signalswere seen with the tester amplicon (FIGS. 15 and 16, lane 6A, derivedfrom infectious HGBV tamarin plasma using total nucleic acid extractionand reverse transcription steps as described in Example 2.B) and theproducts of the three rounds of subtraction/selective amplification(FIGS. 15 and 16, lanes 7A, 8A and 4B referring to the products from thefirst, second and third rounds of subtraction/selective amplification,respectively). These data demonstrate that HGBV clones 2 (SEQUENCE I.D.NO. 22) and 16 (SEQUENCE I.D. NO. 26) can be detected in nucleic acidsequences amplified from infectious sources; HGBV clones 2 (SEQUENCEI.D. NO. 22) and 16 (SEQUENCE I.D. NO. 26) are not derived from tamarin,human, yeast or E. coli genomic DNA sequences.

B. Genomic PCR Analysis

To further demonstrate the exogenicity of the HGBV sequences and supporttheir viral origin, PCR was performed on genomic DNA from tamarin,human, yeast and E. coli. DNA from normal tamarin kidney and livertissue was prepared as described by J. Sambrook et al., supra. Yeast,Rhesus monkey kidney and human placental DNAs were obtained fromClontech. E. coli DNA was obtained from Sigma.

PCR was performed using GeneAmp® reagents from Perkin-Elmer-Cetusessentially as directed by the supplier's instructions. Briefly, 300 ngof genomic DNA was used for each 100 μl reaction. PCR primers derivedfrom HGBV cloned sequences (for clone 2, SEQUENCE I.D. NOS. 87 and 88;for clone 4, SEQUENCE I.D. NOS. 89 and 90; for clone 10, SEQUENCE I.D.NOS. 91 and 92; for clone 16, SEQUENCE I.D. NOS. 93 and 94; for clone18, SEQUENCE I.D. NOS. 95 and 96; for clone 23, SEQUENCE I.D. NOS. 97and 98; and for clone 50, SEQUENCE I.D. NOS. 99 and 100) were used at afinal concentration of 0.5 μM. PCR was performed for 35 cycles (94° C.,1 min; 55° C., 1 min; 720C, 1 min) followed by an extension cycle of 72°C. for 7 min. The PCR products were separated by agarose gelelectrophoresis and visualized by UV irradiation after direct stainingof the nucleic acid with ethidium bromide and/or hybridizaion to aradiolabelled probe after Southern blot transfer to a nitrocellulosefilter. Probes were generated as described in Example 6A. Filters wereprehybridized in Fast-Pair Hybridization Solution from Digene(Belstville, Md.) for 3-5 hours and then hybridized in Fast-PairHybridization Solution with 100-200 cpm/cm² at 42° C. for 15-25 hours.Filters were washed as described in G. G. Schlauder et al., J. Virol.Methods 37:189-200 (1992) and exposed to Kodak X-Omat-AR film for 15 to72 hours at −70° C. with intensifying screens.

FIG. 17 shows an ethidium bromide stained 1.5% agarose gel. FIG. 18shows an autoradiogram from a Southern blot from the same gel afterhybridization to the radiolabeled probe from clone 16 (SEQUENCE I.D. NO.26). Consistent with its exogenous nature, clone 16 (SEQUENCE I.D. NO.26) sequences were not detected in tamarin (FIGS. 17 and 18, lanes 9 and10), Rhesus monkey (lane 11) or human genomic DNAs (lane 12) or in yeastor E. coli DNAs (data not shown) by genomic PCR analysis despite beingable to detect clone 16 (SEQUENCE I.D. NO. 26) sequences that have beenspiked into normal tamarin liver and kidney DNA at 0.05 genomeequivalents (lanes 17 and 18). In addition, primers derived from thehuman dopamine D1 receptor gene, 1000-1019 base pairs (sense primer) and1533-1552 base pairs (antisense primer) (GenBank accession numberX55760, R. K. Sunahara. et al., Nature 347:80-83 [1990]) successfullyamplified the dopamine D1 receptor DNA from the primate genomic DNAs(FIG. 17 lanes 2, 3, 4 and 5 corresponding to tamarin kidney, tamarinliver, rhesus monkey and human DNAs) demonstrating the utility of thismethod for detecting low copy number (i.e. single copy) sequences. Lanes1 and 8 are H₂O contols for dopamine D1 receptor and clone 16 primers(SEQUENCE I.D. NOS. 93 and 94), respectively. Lane 6 contains 100 fg ofclone 16 (SEQUENCE I.D. NO. 26) plasmid DNA amplified with the dopaminereceptor primers. Lanes 14, 15, 16 and 20 contain 1, 3, 10, and 100 fg,respectively, of clone 16 (SEQUENCE I.D. NO. 26) plasmid DNA. Lanes 7and 19 are markers. Similar results were obtained using PCR primersspecific for clones 2, 4, 10, 18, 23 and 50 described above (data notshown). Clones 2 (SEQUENCE I.D. NO. 22), 4 (SEQUENCE I.D. NO. 21), 10(SEQUENCE I.D. NO. 23), 18 (SEQUENCE I.D. NO. 27), 23 (SEQUENCE I.D. NO.28) and 50 (SEQUENCE I.D. NO. 29) are inconclusive at this time.However, clones 4 (SEQUENCE I.D. NO. 21), 10 (SEQUENCE I.D. NO. 23), 18(SEQUENCE I.D. NO. 27) and 50 (SEQUENCE I.D. NO. 29) sequences were notdetected in tamarin, human, yeast and E. coli DNA, (Rhesus monkey wasnot tested) indicating that these sequences are exogenous to the genomicDNA sources tested and supporting the viral origin of these sequences.

Example 7 Presence of HGBV Sequences in Tamarin Sera

The presence of the HGBV clone sequences in pre-inoculation and acutephase T-1053 plasma was examined by PCR. Because the HGBV genome couldbe DNA or RNA, PCR and RT-PCR was performed. Specifically, total nucleicacids were extracted from plasma as described in Example 3(A). PCR wasperformed on the equivalent of 5 μl plasma nucleic acids as described inExample 6(B) and RT-PCR was performed using the GeneAmp® RNA PCR Kitfrom Perkin-Elmer-Cetus essentially according to the manufacturer'sinstructions using 1 μM concentration of primers (for clone 2, SEQUENCEI.D. NOS.87 and 88; for clone 4, SEQUENCE I.D. NOS. 89 and 90; for clone10, SEQUENCE I.D. NOS. 91 and 92; for clone 16, SEQUENCE I.D. NOS. 93and 94; for clone 18, SEQUENCE I.D. NOS. 95 and 96; for clone 23,SEQUENCE I.D. NOS. 97 and 98; and for clone 50, SEQUENCE I.D. NOS. 99and 100) in the PCRs. cDNA synthesis was primed with random hexamers.

Ethidium bromide staining and hybridization of the PCR productsdemonstrated the presence of HGBV clone sequences 2 (SEQUENCE I.D. NO.22), 4 (SEQUENCE I.D. NO. 21), 10 (SEQUENCE I.D. NO. 23), 16 (SEQUENCEI.D. NO. 26), 18 (SEQUENCE I.D. NO. 27), 23 (SEQUENCE I.D. NO. 28) and50 (SEQUENCE I.D. NO. 29) in the acute phase T-1053 plasma and not thepre-inoculation T-1053 plasma (data not shown). In addition, HGBV clones2 (SEQUENCE I.D. NO. 22), 4 (SEQUENCE I.D. NO. 21), 10 (SEQUENCE I.D.NO. 23), 18 (SEQUENCE I.D. NO. 27), 23 (SEQUENCE I.D. NO.28) and 50(SEQUENCE I.D. NO. 29) sequences could be detected in H205, the HGBVinoculum that was injected into tamarin T-1053 (see Example 1B). Theseresults are summarized in TABLE 8. It should be noted that the HGBVclone sequences were only detected by RT-PCR in the acute phase plasma.The fact that the HGBV clone sequences were detected in the acute phaseplasma by PCR only after a reverse transcription step to convert RNA tocDNA, taken together with the limited homology of some of these cloneswith HCV isolates, and the presence of the sequences coding for theconserved amino acids found in the RNA-dependent RNA polymerase in HGBVclone 10 (SEQUENCE I.D. NO. 23; Example 5) suggest that HGBV is an RNAvirus.

RT-PCR analysis of a panel of tamarin plasmas with HGBV clone 16sequence (SEQUENCE I.D. NO. 26) was undertaken to confirm the presenceof HGBV clone 16 (SEQUENCE I.D. NO. 26) in other individuals who hadbeen experimentally infected with HGBV. Briefly, nucleic acids wereisolated as previously described (G. G. Schlauder et al., J. VirologicalMethods 37:189-200 [1992]) from 25 μl of plasma from tamarins obtainedprior to and after experimental infection with the H205 inoculum.Ethanol precipitated nucleic acids were resuspended in 3 μl ofDEPC-treated H₂O. cDNA synthesis and PCR were performed using theGeneAmp RNA PCR Kit from Perkin-Elmer-Cetus essentially according to themanufacturer's instructions. cDNA synthesis was primed with randomhexamers. The resulting cDNA was subjected to PCR using clone 16 primers(SEQUENCE I.D. NOS. 93 and 94) at a final concentration of 0.5 μM. PCRwas performed for 35 cycles (94° C., 1 min; 55° C., 1 min; 72° C., 1min) followed by an extension cycle of 72° C. for 7 min. The PCRproducts were separated by agarose gel electrophoresis and visualized byUV irradiation after direct staining of the nucleic acid with ethidiumbromide and/or hybridization to a radiolabelled probe after Southernblot transfer to a nitrocellulose filter as describes in Example 6B.

FIG. 19 shows an ethidium bromide stained 1.5% agarose gel. FIG. 20shows an autoradiogram from a Southern blot from the same gel afterhybridization to the radiolabeled probe from clone 16 (SEQUENCE I.D. NO.26). H₂O and normal human serum are shown in lanes 1 and 2. Lanes 3, 19and 20 are markers. Lanes 4, 8, 12,and 16 are from uninfected tamarinsera while lanes 6, 10, 14 and 18 are from infected tamarin sera. Theseresults show that HGBV clone 16 sequence (SEQUENCE I.D. NO. 26) wasdetected in other individuals infected with HGBV, in addition to tamarinT-1053, and not in uninfected individuals. Acute phase sera from fiveH205-infected animals were tested. Clone 16 sequences (SEQUENCE I.D. NO.26) were detected in sera from three of these animals [lane 10, T-1049,14 days post-inoculation (dpi); lane 14, T-1051, 28 dpi; lane 18,T-1055, 16 dpi.]. The clone 16 sequence (SEQUENCE I.D. NO. 26) was notdetected in pre-inoculation sera from any of the five animals (lane 4,T-1048; lane 8, T1049; lane 12, T-1051; lane 16, T-1055; T-1057 notshown). These results suggest that the clone 16 sequence (SEQUENCE I.D.NO. 26) may be derived from the infectious HGBV agent. The absence ofclone 16 sequence (SEQUENCE I.D. NO. 26) in two of five acute phaseplasmas (lane 6, T-1048, 28 dpi; T-1057, 14 dpi, not shown) may beexplained by the relative low sensitivity of the clone 16 RT-PCR(estimated to be able to detect approximately ≧1000 copies of clone 16sequence (SEQUENCE I.D. NO. 26) coupled with the acute resolving natureof HGBV infection in tamarins. Thus, the acute plasma from the twonegative animals may contain a titer of HGBV that is below the detectionlevel of the RT-PCR assay employed. The observation that these twoanimals were positive for clone 4 (SEQUENCE I.D. NO.21) by RT-PCR(Example 14) may reflect the presence of RNA sequences of one virus(containing clone 4) and the absence of detectable RNA sequences from asecond virus (containing clone 16).

Example 8 Northern Blot Analysis of HGBV Sequences in Infected TamarinLiver

Because the HGBV clone sequences were detectable by RT-PCR in the acutephase tamarin plasma and the H205 inoculum, it was likely that thesesequences originate from the HGBV genome. Additional RT-PCR studiesdemonstrated the presence of the HGBV sequences in liver RNA extractedfrom the H205-infected tamarin, T-1053 (data not shown). Therefore, todetermine the size of the HGBV genome, Northern analysis ofH205-infected and uninfected tamarin liver RNA was performed. Totalcellular RNA was extracted from 1.25 g liver of H205-infected tamarinT-1053 and from 1.0 g of liver from a control (i.e. uninfected) tamarinT-1040 using an RNA isolation kit (Stratagene, La Jolla, Calif.) asdirected by the manufacturer. Total RNA (30 μg) was electrophoresedthrough a 1% agarose gel containing 0.6 M formaldehyde (R. M. Fourney,et al., Focus 10: 5-7, [1988]) and then transferred to Hybond-N nylonmembrane (Amersham) by capillary action in 20×SCC (pH 7.0) as previouslydescribed. J. Sambrook, et al., Molecular Cloning—A Laboratory Manual,2nd Edition (1989). The RNA was UV-crosslinked to the nylon membranewhich was then baked in a vacuum oven at 80° C. for 60 min. The blotswere prehybridized at 60° C. for 2 hours in 25 ml of a solutioncontaining 0.05 M PIPES, 50 mM sodium phosphate, 100 mM NaCl, 1 mM EDTA,and 5% SDS. G. D. Virca, et al., Biotechniques 8:370-371 (1990). Priorto hybridization with the radiolabeled DNA probe, the solution wasremoved and 10 ml of fresh solution was added. The probes used forhybridization were clone 4 (SEQUENCE I.D. NO. 21; 221 bp) and clone 50(SEQUENCE I.D. NO. 29; 337 bp) and the 2000 bp cDNA encoding humanβ-actin. P. Gunning, et al., Mol. and Cell. Biol. 3:787-795 (1983). Theprobes (50 ng) were radiolabeled using a random primer labeling kit(Stratagene. La Jolla, Calif.) in the presence of [α-³²P]dATP asdirected by the manufacturer. The specific activity of each probe wasapproximately 10⁹ cpm/μg. The blots were hybridized at 60° C. for 16hours and washed as described (G. D. Virca, et al., supra) and thenexposed to Kodak X-Omat-AR film at −80° C. Photographs of the resultingautoradiographs are shown in FIG. 21A. Lanes 1, 3, and 5 contain liverRNA from T-1040 and lanes 2, 4, and 6 contain liver RNA from T-1053.Lanes 1 and 2 were hybridized with the human β-actin cDNA probe; lanes 3and 4 were hybridized with the clone 4 probe (SEQUENCE I.D. NO. 21); andlanes 5 and 6 were hybridized with the clone 50 probe (SEQUENCE I.D. NO.29). Exposure times were as follows: lanes 1 and 2, 5 hours at −80° C.;lanes 3-6, 56 hours at −80° C. The positions of the 28S and 18Sribosomal RNAs are indicated by the arrows. The relative sizes of theseribosomal RNAs are 6333 and 2366 nucleotides, respectively. J. Sambrook,et al., supra.

Clone 4 (SEQUENCE I.D. NO. 21) and clone 50 probes (SEQUENCE I.D. NO.29) hybridized with an RNA species present in RNA extracted from theliver of the infected tamarin (T-1053) (FIG. 21A, lanes 4 and 6). Thesize of this hybridizable RNA species was calculated at approximately8300 nucleotides based on its relative mobility with respect to 28S and18S ribosomal RNAs. Both probes appear to hybridize to the same RNAspecies. Neither probe hybridized with RNA extracted from the liver ofthe uninfected tamarin (T-1040) (FIG. 21A, lanes 3 and 5). These resultssuggest that the sequences of clones 4 (SEQUENCE I.D. NO. 21) and 50(SEQUENCE I.D. NO. 29) are present within the same 8.3 Kb transcript.

In order to determine the strandedness of the HGBV RNA genome,strand-specific radiolabeled DNA probes were prepared by assymetric PCRusing the GeneAmp® PCR kit from Perkin-Elmer essentially according tothe manufacturer's instructions. Purified clone 50 DNA (SEQUENCE I.D.NO. 29) was used as template in separate reactions containing either theclone 50 negative strand-specific primer (SEQUENCE I.D. NO. 99) or theclone 50 positive strand-specific primer (SEQUENCE I.D. NO. 100) at 1 μMfinal concentrations. The reaction mixture contained [α³²P-dATP](Amersham; 3000 Ci/mmol) in place of the dATP normally included in thereaction mixture. Following 30-cycles of linear amplification of thetemplate, the unincorprated [α³²P-dATP] was removed by Quick-Spin®Sephadex G50 spin columns (Boehringer-Mannheim, Indianapolis, Ind.)according to the manufacturer's instructions. Hybridization of theradiolabeled probes to DNA dot blots containing ten-fold serialdilutions of double-stranded clone 50 DNA (SEQUENCE I.D. NO. 29)demonstrated that the two probes possessed nearly identicalsensitivities (data not shown). The radiolabled probes were thenhybridized to RNA blots containing 30 μg of total liver RNA extractedfrom uninfected tamarin T-1040 and from infected tamarin T-1053 asdescribed above. Photographs of the resulting autoradiographs are shownin FIG. 21B. Lanes 1 and 3 contain liver RNA from T-1040 and lanes 2 and4 contain liver RNA from T-1053. Lanes 1 and 2 were hybridized with theclone 50 positive strand probe (i.e., the positive strand isradiolabeled and will detect the negative strand; SEQUENCE I.D. NO.100); lanes 3 and 4 were hybridized with the clone 50 negative strandprobe (i.e., the negative strand is radiolabeled and will detect thepositive strand; SEQUENCE I.D. NO.99). The blots were exposed for 18hours at −80° C. The positions of the 28S and 18S ribosomal RNAs areindicated by the arrows.

As shown in FIG. 21B, the clone 50 positive and negative strand probes(SEQUENCE I.D. NOS. 100 and 99, respectively) hybridized to an RNAspecies of approximately 8.3 kilobases extracted from the liver of theinfected tamarin T-1053 (FIG. 21B, lanes 2 and 4), but not to RNAextracted from the liver of the uninfected tamarin T-1040 (FIG. 21B,lanes 1 and 3). This is consistent with the Northern blot resultsobtained with the clone 4 (SEQUENCE I.D. NO. 21) and clone 50 (SEQUENCEI.D. NO. 29) double-stranded probes shown above. The more intense signalobtained with the clone 50 negative strand probe (SEQUENCE I.D. NO. 99)(FIG. 21B, lane 4 vs. lane 2) suggests that the predominant RNA speciespresent in the liver of infected tamarins is the positive (i.e. coding)strand.

Example 9 Extending the HGBV Clone Sequence

A. Generation of HGBV Sequences

The clones obtained as described in Example 3 and sequenced as describedin Example 5 hereinabove appear to be derived from separate regions ofthe HGBV genome. Therefore, to obtain sequences from additional regionsof the HGBV genome that reside between the previously identified clones,and to confirm the sequence of the RDA clones, several PCR walkingexperiments were performed.

Total nucleic acids were extracted from 50 μl aliquots of infectiousT-1053 plasma as described in Example 3(A). Briefly, precipitatednucleic acids were resuspended in 10 μl DEPC-treated H₂O. StandardRT-PCR was performed using the GeneAmp® RNA PCR kit (Perkin Elmer) asdirected by the manufacturer. Briefly, PCR was performed on the cDNAproducts of random primed reverse transcription reactions of theextracted nucleic acids with 2 mM MgCl₂ and 1 μM primers. Reactions weresubjected to 35 cycles of denaturation-annealing-extension (94° C., 30sec; 55° C., 30 sec; 72° C. 2 min) followed by a 3 min extension at 72°C. The reactions were held at 4° C. prior to agarose gel analysis. Theseproducts were cloned into pT7 Blue T-vector plasmid (Novagen) asdescribed in the art. TABLE 9 presents the results obtained when thesereactions were peformed.

TABLE 9 Reaction Primer 1 Primer 2 Product Size 1.1 SEQ ID #88 comp. ofSEQ ID #93 878 bp 1.2 comp. of SEQ ID #87 SEQ ID #97 1191 bp  1.3 SEQ ID#90 SEQ ID #101 864 bp 1.4 comp. of SEQ ID #99 comp. of SEQ ID #102  1.4kb 1.5 SEQ ID #102 SEQ ID #91 672 bp 1.6 SEQ ID #98 SEQ ID #99 2328 bp 1.7 comp of SEQ ID #103 SEQ ID #104 1300 bp  1.8 comp. of SEQ ID #105SEQ ID #87 900 bp 1.9 SEQ. ID. #93 SEQ. ID. #99 2323 bp  1.10 SEQ. ID.#92 SEQ. ID. #91 1216 bp  1.11 SEQ. ID. #90 SEQ. ID. #92 1570 bp  1.12comp. of SEQ ID #106 SEQ ID #103 550 bp 1.13 comp. of SEQ ID #107 SEQ ID#108 900 bp 1.14 SEQ ID #107 comp. of SEQ ID #96 1100 bp  1.15 comp. ofSEQ ID #109 SEQ ID #110 410 bp 1.16 SEQ ID #111 comp. of SEQ #112 600 bp1.17 comp. of SEQ ID #113 SEQ ID #114 1000 bp  1.18 SEQ ID #98 comp. ofSEQ ID #115 720 bp 1.19 comp. of SEQ ID #116 comp. of SEQ ID #117 825 bp1.20 SEQ ID #118 comp. of SEQ ID #119 700 bp 1.21 SEQ ID #120 SEQ ID #95900 bp 1.22 SEQ ID #121 comp. of SEQ ID #122 950 bp 1.23 SEQ ID #123 SEQID #124 420 bp 1.24 SEQ.ID #87 SEQ.ID #88 130 bp 1.25 SEQ.ID #55 SEQ.ID#89 450 bp

A modification of a PCR walking technique described by Sorensen et al.(J. Virol. 67:7118-7124 [1993]) was utilized to obtain additional HGBVsequences. Briefly, total nucleic acid were extracted from infectioustamarin T-1053 plasma and reverse transcribed. The resultant cDNAs wereamplified in 50 μl PCR reactions (PCR 1) as described by Sorensen et al.(supra) except that 2 mM MgCl₂ was used. The reactions were subjected to35 cycles of denaturation-annealing-extension (94° C., 30 sec; 55° C.,30 sec; 72° C., 2 min) followed by a 3 min extension at 72° C.Biotinylated products were isolated using streptavidin-coatedparamagnetic beads (Promega) as described by Sorensen et al. (supra).Nested PCRs (PCR 2) were performed on the streptavidin-purified productsas described by Sorensen et al. for a total of 20 to 35 cycles ofdenaturation-annealing-extension as described above. The resultantproducts and the PCR primers used to generate them are listed in TABLE10.

TABLE 10 Reaction product Primer set PCR 1 Primer set PCR 2 Size of PCR2.1 SEQ ID #103/SEQ ID #125 SEQ ID #668/SEQ ID #126 500 bp 2.2 SEQ ID#114/SEQ ID #125 SEQ ID #105/SEQ ID #126 1000 bp  2.3 SEQ ID #92/SEQ ID#125 SEQ ID #123/SEQ ID #126 400 bp 2.4 SEQ ID #127/SEQ ID #128 comp. ofSEQ ID #88/ 420 bp SEQ ID #126 2.5 SEQ ID #108/SEQ ID #128 SEQ ID#106/SEQ ID #126 900 bp 2.6 SEQ ID #129/SEQ ID #125 SEQ ID #98/SEQ ID#126 750 bp 2.7 SEQ ID #116/SEQ ID #128 SEQ ID #115/SEQ ID #126 825 bp2.8 SEQ ID #130/SEQ ID #125 SEQ ID #107/SEQ ID #126 630 bp 2.9 SEQ ID#110/SEQ ID #135 SEQ ID #131/SEQ ID #126 390 bp 2.10 SEQ ID #132/SEQ ID#125 SEQ ID #109/SEQ ID #126 1000 bp  2.11 SEQ ID #111/SEQ ID #128 SEQID #133/SEQ ID #126 600 bp 2.12 SEQ ID #134/SEQ ID #135 SEQ ID #112/SEQID #126 580 bp 2.13 SEQ ID #136/SEQ ID #125 SEQ ID #137/SEQ ID #126 400bp 2.14 SEQ ID #138/SEQ ID #128 SEQ ID #113/SEQ ID #126 500 bp 2.15 SEQID #139/SEQ ID #128 SEQ ID #140/SEQ ID #126 900 bp 2.16 SEQ ID #121/SEQID #135 SEQ ID #141/SEQ ID #126 400 bp 2.17 SEQ ID #142/SEQ ID #125comp. of SEQ ID #102/ 1000 bp  SEQ ID #126 2.18 SEQ ID #143/SEQ ID #135SEQ ID #144/SEQ ID #126 550 bp 2.19 SEQ.ID #87/SEQ ID #125 SEQ.ID#90/SEQ ID #126 220 bp

These products were isolated from low melting point agarose gels andcloned into pT7 Blue T-vector plasmid (Novagen) as described in the art.

RNA ligase-mediated 5′ RACE (rapid amplification of cDNA ends) wasemployed to obtain the 5′ end sequences from viral genomic RNAs asdescribed hereinabove. Briefly, the 5′ AmpliFINDER™ RACE kit (Clontech,Palo Alto, Calif.) was used as directed by the manufacturer. The sourceof the viral RNA was acute phase T-1053 plasma that was extracted asdescribed above. The virus-specific oligonucleotides utilized for thereverse transcription (RT), the first PCR amplification (PCR 1) and thesecond PCR amplification (PCR 2) are listed in TABLE 11. The ligatedanchor primer and its complementary PCR primer were provided by themanufacturer. PCRs were performed with the GeneAmp® PCR kit (PerkinElmer) as directed by the manufacturer.

TABLE 11 Size of PCR 2 Reaction RT primer PCR 1 primer PCR 2 primerproduct 3.1 SEQ ID #145 SEQ ID #146 SEQ ID #147 190 bp 3.2 SEQ ID #148SEQ ID #149 SEQ ID #150 620 bp

The products generated by RNA ligase-mediated 5′ RACE were isolated fromlow melting point agarose gels and cloned into pT7 Blue T-vector plasmid(Novagen) as described in the art.

To obtain additional sequence at the 5′ and 3′ ends of HGBV-B SEQUENCE(see below, Evidence for the existence of two HCV-like flaviviruses inHGBV), an RNA circularization experiment was performed. (This method isbased on that described by C. W. Mandl et al. (1991) Biotechniques, Vol10 (4): 485-486.) Total nucleic acids were purified from 50 μl of T-1057plasma (14 days post H205 inoculation except that 1 μg glycogen replacedthe tRNA in the precipitation. The nucleic acid pellet was dissolved in16.3 μl of DEPC-treated water, and 25 μl of 2×TAP buffer (1×=50 mMNaOAC, pH 5.0, 1 mM EDTA, 10 mM 2-mercaptoethanol, 2 mM ATP) and 8.7 μlof tobacco acid pyrophophatase (20 Units; Sigma) were added. The mixturewas incubated at 37° C. for 60 min. The sample was extracted with phenol(water-saturated) followed by chloroform and then precipitated withNaOAC/EtOH in the presence of glycogen (1 μg). The pellet was dissolvedin 83 μl of DEPC water and 10 μl of 10×RNA ligase buffer (New EnglandBiolabs, NEB), 2 μl of RNase inhibitor (Perkin Elmer), and 5 μl of T4RNA ligase (NEB) was then added. The mixture was incubated at 4° C. for16 hours. The sample was then extracted with phenol (water-saturated)and then chloroform as before and then precipitated with NaOAC/EtOH.

One-tenth of the ligated RNA was used in the reverse transcriptase (RT)reaction using Superscript RT (GIBCO/BRL) and SEQUENCE ID. NO. 146 asthe primer as directed by the manufacturer. One-half of the RT reactionmix was used for PCR1 in the presence of a biotinylated oligonucleotideprimer (SEQUENCE ID. NO. 146) and and a second oligonucleotide primer(SEQUENCE ID. NO. 133) as described above. PCR1 products were purifiedfrom the reaction mixture using streptavidin-magnetic beads as describedby Sorensen et al. Purified PCR1 products (2 μl out of 30 μl) were usedas the template for PCR2. PCR2 using oligonucleotide primers (SEQUENCEID. NOS. 147 and 154) yielded a 1200 bp product that was cloned into pT7Blue T-vector plasmid and sequenced as described below. Sequenceanalysis of two independent clones from this experiment demonstrated100% identity in the region of overlap with known sequence (although oneclone possessed a sequence of 18 T residues and the other a sequence of27 T residues), and an additional 270 bases of new sequence.

The above circularization experiment provided sequence from both the 5′-and 3′-ends of the HGBV-B viral genome that was not obtained usingstandard 3′- or 5′-RACE techniques. However, the exact 5′-3′ junction isdifficult to determine even after additional PCR experiments areperformed using primers designed from the newly obtained sequence. Thus,in order to better characterize the 5′-end of the HGBV-B RNA genome aprimer extension experiment was performed using RNA isolated from theliver of T-1053.

Total cellular RNA was isolated from the liver of T-1053 and a control(i.e. uninfected) animal (T-1040) as described in Example 7. Anantisense oligonucleotide (SEQUENCE I.D. NO. 155) was endlabeled withγ-³²P-ATP using T4 polynucleotide kinase (NEB) to a specific activity ofapproximately 9.39×10⁷ CPM/μg as described (Sambrook et al.). The primerwas annealed to 30 μg of T-1053 and T-1040 liver RNA in separatereactions and then extended using MMLV reverse transcriptase(Perkin-Elmer) as previously described (Sambrook et al). The productswere analyzed on a 6% sequencing gel. A sequence ladder generated fromone of the HGBV-B circularization clones using the same primer as thatutilized for the primer extension served as a size standard.

Primer extension products of 176 bp were obtained from T-1053. Theseproducts were not obtained when primer extension was performed usingliver RNA from an uninfected animal (T-1040) and therefore representproducts derived from the HGBV-B genome. The length of the productsobtained indicate that the 5′-end of the genome, as present in the liverof infected animals, is located 442 nucleotides upstream of theinitiator AUG codon.

To confirm the 3′ location of the sequence obtained in thecircularization experiment, RT-PCRs were performed using primersdesigned to the predicted 3′ termini (see reaction 1.25, TABLE 2).RT-PCR of infectious T-1053 plasma as (described above) using SEQUENCEID. NOS. 156 and SEQUENCE ID. NO. 157 yielded a product of 450 bp. Incontrast, RT-PCR using the complement of SEQUENCE ID. NO.157 andSEQUENCE ID. NO. 147 did not yield a detectable PCR product (data notshown). These data suggest that the 3′ end of the genome is located 50nucleotides downstream of the poly T tract.

The cloned products from TABLES 9, 10 and 11, and the RNAcircularization experiment were sequenced as previously described inExample 5. Interestingly, the cloned products of reactions 1.4, 1.6,1.9, 1.10 and 1.11 were found to contain only one of the two primersequences at the termini, suggesting that these products were the resultof false priming events. PCR/sequencing experiments have linkedsequences detected in products 1.4, 1.6, 1.9, 1.10 and 1.11 with clone 4(SEQUENCE I.D. NO. 21) and/or clone 50 (SEQUENCE I.D. NO. 29). Inaddition, sequences derived from each of these reactions contain limitedHCV identity. Thus, these products, although a result of false primingat one end of the PCR product, appear to contain authentic HGBVsequence. The product from reaction 1.14 also appeared to be a result offalse priming. Here, the complement of SEQUENCE I.D. NO. 160 is found atthe 5′ end of the product from reaction 1.14 (GB-B, FIG. 22). This wasunexpected because SEQUENCE I.D. NO. 160 was derived from SEQUENCE I.D.NO. 161 which resides in GB-A. However, the sequence identity betweenproducts from reactions 1.14 and 2.8, together with additionalPCRs/sequencing experiments (data not shown), demonstrate that reaction1.14 contains authentic HGBV sequence. Apparently, the complement ofSEQUENCE I.D. NO. 160 had enough identity to GB-B sequences upstream ofSEQUENCE I.D. NO. 162 to act as a PCR primer.

The sequences obtained from the products described in TABLES 9, 10 and11 hereinabove, and the RNA circularization experiment were assembledinto contigs using the GCG Package (version 7) of programs. A schematicof the assembled contigs is presented in FIG. 22). GB contig A (GB-A) is9493 bp in length, all of which has been sequenced and is presented inSEQUENCE I.D. NO. 163. GB-A includes clones 2 (SEQUENCE I.D. NO. 22), 16(SEQUENCE I.D. NO. 26), 23 (SEQUENCE I.D. NO. 28), 18 (SEQUENCE I.D. NO.27), 11 (SEQUENCE I.D. NO. 24) and 10 (SEQUENCE I.D. NO. 23). SEQUENCEI.D. NO. 163 was translated into three possible reading frames and ispresented in the Sequence Listing as SEQUENCE I.D. NOS. 164-392. GBcontig B (GB-B) is 9143 bp and is presented in SEQUENCE I.D. NO. 393.GB-B (SEQUENCE I.D. NO. 393) includes clones 4 (SEQUENCE I.D. NO. 21),50 (SEQUENCE I.D. NO. 29), 119 (SEQUENCE I.D. NO. 30) and 13 (SEQUENCEI.D. NO. 25). SEQUENCE I.D. NO. 393 was translated into one open readingframe and is presented in the Sequence Listing as SEQUENCE I.D. 396 and397. The UTRs from the 5′ and the 3′ ends can each be translated intosix reading frames.

B. Evidence for the Existence of Two HCV-Like Viruses in HGBV

1. Evidence for GB-A and GB-B Representing Two Distinct RNA Species

Comparison of GB-A (SEQUENCE I.D. NO. 163) GB-B (SEQUENCE I.D. NO. 393)and HCV-1 (GenBank accession # M67463) demonstrate that GB-A (SEQUENCEI.D. NO. 163), GB-B (SEQUENCE I.D. NO. 393) and HCV-1 are all distinctsequences. Dot plot analyses of the nucleic acid sequences of GB-A(SEQUENCE I.D. NO. 163), GB-B (SEQUENCE I.D. NO. 393) and HCV-1 wereperformed using the GCG Package (version 7). Using a window size of 21and a stringency of 14, GB-A (SEQUENCE I.D. NO. 163), GB-B (SEQUENCEI.D. NO. 393) and HCV-1 were found to clearly contain differentnucleotide sequences (FIG. 23). Therefore, GB-A (SEQUENCE I.D. NO. 163)and GB-B (SEQUENCE I.D. NO. 393) do not represent different strains orgenotypes of HCV or of each other. Short regions of limited nucleotideidentity are found in the putative NS3-like and NS5b-like sequences ofGB-A (SEQ. ID. NO. 163) and GB-B (SEQ. ID. NO. 393) and the NS3 and NS5bsequences of HCV by this analysis. However, nucleotide identity in theseregions is not surprising because NS3 and NS5b code for the putativeNTP-binding helicase and the RNA-dependent RNA polymerase, respectively,which are conserved in all flaviviruses (see below). That GB-A (SEQUENCEI.D. NO. 163) and GB-B (SEQUENCE I.D. NO. 393) represent separate RNAmolecules and not different regions of the same RNA molecule isevidenced by the 5′ RACE experiments (above) and supported by theNorthern blot data (as described in Example 8. First, the 5′ RACEexperiments show distinct 5′ ends for GB-A (SEQUENCE I.D. NO. 163) andGB-B (SEQUENCE I.D. NO. 393). Because RNA molecules can contain only one5′ end, GB-A (SEQUENCE I.D. NO. 163) and GB-B (SEQUENCE I.D. NO. 393)represent separate RNA molecules. Second, the 8300 base RNA moleculedetected in infected tamarin liver RNA by probing Northern blots withclones 4 and 50 (SEQUENCE I.D. NOS. 21 and 29, respectively, both fromGB-B [SEQUENCE I.D. NO. 393], see Example 8, corresponds closely to thesize of GB-B (SEQUENCE I.D. NO. 393, 9143 bp). If GB-A and GB-B werepart of the same RNA molecule, one would expect a Northern blot productof at least 17,000 bases. These data demonstrate that GB-A (SEQUENCEI.D. NO. 163) and GB-B (SEQUENCE I.D. NO. 393) represent the nucleotidesequences of two distinct RNA molecules that are not variants of HCV oreach other.

Northern blot analysis and PCR studies of T-1053 provided evidence thatthe two RNA species corresponding to GB-A (SEQUENCE I.D. NO. 163) andGB-B (SEQUENCE I.D. NO. 393) were not at equivalent levels in the liver.As stated above, clones 4 and 50 (SEQUENCE I.D. NOS. 21 and 29,respectively), both from the GB-B (SEQUENCE I.D. NO. 393), hybridized toan 8.3 kb RNA species present in infected liver of T-1053 (as describedin Example 8). In contrast, clones 2 (SEQUENCE I.D. NO. 22), 10(SEQUENCE I.D. NO. 23), 16 (SEQUENCE I.D. NO. 26 and 23 (SEQUENCE I.D.NO. 28), all from GB-A (SEQUENCE ID. NO. 163), showed no hybridizationwith T-1053 liver RNA in identical experiments (data not shown). Inaddition, clone 16 PCR generated much less product than clone 4 PCR oncDNAs generated from T-1053 liver RNA by ethidium staining, despiteequivalent sensitivities of clone 4 and clone 16 PCRs demonstrated usingplasmid templates (data not shown). This is in contrast to what is foundin T-1053 plasma at the time of sacrifice. PCR titration experiments forclone 4 (GB-B-specific, SEQUENCE I.D. NO. 393) and clone 16(GB-A-specific, SEQUENCE I.D. NO. 163) PCR on cDNAs generated fromT-1053 plasma RNA suggest that equivalent amounts of GB-A (SEQUENCE I.D.NO. 163) RNA and GB-B (SEQUENCE I.D. NO. 393) RNA are present in T-1053plasma (Example 4, E.2). Thus, although GB-A (SEQUENCE I.D. NO. 163) RNAand GB-B (SEQUENCE I.D. NO. 393) RNA were at equivalent levels in T-1053plasma, there appeared to be a greater amount of GB-B (SEQUENCE I.D. NO.393) RNA relative to GB-A (SEQUENCE I.D. NO. 163) RNA present in T-1053liver at the time of sacrifice. Together, these results provide furtherevidence for the existence of two different RNA molecules correspondingto GB-A (SEQUENCE I.D. NO. 163) and GB-B (SEQUENCE I.D. NO. 393) inT-1053 plasma and suggest that these RNAs are not necessarily present atequivalent levels in infected liver RNA. Therefore, it is unlikely thatGB-A (SEQUENCE I.D. NO. 163) and GB-B (SEQUENCE I.D. NO. 393) make upindividual segments of a single viral genome.

2. Evidence that GB-A (SEQUENCE I.D. NO. 163) and GB-B (SEQUENCE I.D.NO. 393) Represent the Genomes of Two Distinct Viruses

Infectivity and PCR studies provide evidence for the viral nature ofGB-A (SEQUENCE I.D. NO. 163) and B (SEQUENCE I.D. NO. 393).Specifically, tamarins T-1049 and T-1051 which were inoculated withT-1053 plasma that had been filtered (0.1 μm) and diluted to 10⁻⁴, orunfiltered and diluted to 10⁻⁵, respectively, were positive for bothclone 4 (GB-B [SEQUENCE I.D. NO. 393]) and clone 16 (GB-A [SEQUENCE I.D.NO. 163]) sequences. Prior to inoculation, both of these animals werenegative for clones 4 and 16 (Examples 4, E.4 and 4, E.5). Therefore,the two RNA species present in the acute phase T-1053 plasmacorresponding to GB-A and GB-B can be filtered, diluted and passaged toother animals consistent with the proposed viral nature of GB-A(SEQUENCE I.D. NO. 163) and GB-B (SEQUENCE I.D. NO. 393). That GB-A andGB-B represent RNA molecules from separate viral particles is evidencedby PCR studies of the H205-inoculated tamarins. Specifically, four offour tamarins became positive for clone 4 (GB-B [SEQUENCE I.D. NO. 393])by RT-PCR after H205 inoculation. In contrast, only one of 4H205-inoculated tamarins (T-1053) became positive for clone 16 (GB-A[SEQUENCE I.D. NO. 163]) by RT-PCR (Example 4.E.2). Therefore, assumingthat GB-A (SEQUENCE I.D. NO. 163) sequences were truly absent fromT-1048, T-1057 and T-1061, and that the negative clone 16 PCR resultswere not due to poor sensitivity, it would appear that the viruscorresponding to GB-B (SEQUENCE I.D. NO. 393) sequences (i.e. hepatitisGB virus B [HGBV-B]) can be passaged independent of GB-A (SEQUENCE I.D.NO. 163) sequences. An HGBV-B only sample from T-1057 has been passagedtwo additional times (Example 4). GB-A (SEQUENCE I.D. NO. 163) sequenceshave not been detected in these animals by RT-PCR. In addition,significant liver enzyme elevations have been noted in these animals(Example 4), demonstrating that HGBV-B alone caused hepatitis intamarins. GB-A (SEQUENCE I.D. NO. 163) sequences have been identified intamarins lacking detectable GB-B (SEQUENCE I.D. NO. 393) sequences.Specifically, GB-B only animals (T-1048, T-1057 and T-1061) challengedwith T-1053 plasma developed GB-A (SEQUENCE I.D. NO. 163) only viremiasas detected by clone 16 specific RT-PCR. The GB-A only plasma fromT-1057 has been passaged one additional time (Example 4). Thus, itappears that a virus corresponding to GB-A (SEQUENCE I.D. NO. 163)sequences (hepatitis GB virus A [HGBV-A]) can replicate independent ofHGBV-B. Additional passages of HGBV-A in the absence of HGBV-B isongoing. At this time it is not known whether HGBV-A causes hepatitis intamarins. However, the lack of elevated liver enzymes noted in theT-1053 challenged tamarins with HGBV-A viremias and in the passage ofthe HGBV-A only serum from T-1057 argue against the hepatotropic natureof HGBV-B in tamarins.

The presence of two viruses in acute phase T-1053 plasma can be tracedback to the H205 inoculum. Specifically, data from Example 7 showed thatclone 16 (SEQUENCE I.D. NO.26, found in GB-A [SEQUENCE I.D. NO. 163])was absent in the preinoculation plasma from all 7 tamarins tested. Inaddition, clones 2, 10, 18 and 23 (SEQUENCE I.D. NOS. 22, 23, 27 and 28,respectively, all from GB-A [SEQUENCE I.D. NO. 163]) have not beendetected in any pre-HGBV-inoculated tamarin plasma tested (Example 7.Similar negative results were found when preinoculation tamarin plasmawere tested for clones 4 and 50 (SEQUENCE I.D. NOS. 21 and 29,respectively, all from GB-B [SEQUENCE I.D. NO.393]). Thus, both HGBV-Aand HGBV-B were absent in the preinoculation tamarin plasma. Incontrast, all of these clones (i.e. clones 2, 10, 16, 18 and 23 fromGB-A [SEQUENCE I.D. NO. 163], and clones 4 and 50 from GB-B [SEQUENCEI.D. NO. 393]) were detected in the H205 inoculum (TABLE 7).Interestingly, as found in cDNA made from T-1053 liver (above), severaldifferent PCR targets in GB-A (SEQUENCE I.D. NO. 163) all generated lessproduct than similar PCR targets in GB-B (SEQUENCE I.D. NO. 393) usingthe same random primed cDNAs from H205 (data not shown). Thus, weconclude that HGBV-A and HGBV-B are present in the original GB inoculum,H205. However, HGBV-B appears to be more abundant than HGBV-A in H205.The low relative amount of HGBV-A in the H205 inoculum may explain whyonly one of four tamarins were positive for the HGBV-A after H205inoculation (Example 4.E.2).

3. Evidence that HGBV-A and HGBV-B are Members of the Flaviviridae

Searches of the SWISS-PROT database with the three frame translationproducts of GB-A (SEQUENCE I.D. NO. 165-268, 270-384, 386-392) and GB-B(SEQUENCE I.D. NO. 397) as described in Example 5 show limited, butsignificant amino acid sequence identity with various strains of HCV.Translation products from GB-A (SEQUENCE I.D. NO. 164) and GB-B(SEQUENCE I.D. NO. 393) show the closest homology to regions of thenonstructural proteins of various HCV isolates (i.e. NS2, NS3, NS4 andNS5). For example, as shown in FIG. 24, the conserved residues(indicated by *) in the putative NTP-binding helicase domain offlaviviruses (FIG. 24A) and in the RNA-dependent RNA polymerase domainof all viral RNA-dependent RNA polymerases (FIG. 24B) are held in commonbetween HCV-1 NS3 and NS5b (SWISS-PROT accession number p26664),respectively, and the predicted translation products of GB-A (SEQUENCEI.D. NO. 390) and GB-B (SEQUENCE I.D. NO. 397). (See Choo et al., PNAS88:2451-2455 [1991] and Domier et al., Virology 158:20-27 [1987]).Therefore, it appears that both GB-A virus and GB-B virus encodefunctional NTP-binding helicases and RNA-dependent RNA polymerases.However, GB-A (SEQUENCE I.D. NO. 390) and GB-B (SEQUENCE I.D. NO. 397)do not share complete amino acid identity to each other and/or to HCV inother regions of HCV NS3 and NSSb. Specifically, over the 200 residueregion of NS3 shown in FIG. 24A, GB-A (SEQUENCE I.D. NO. 390, residues1252-1449) virus and HCV-1 (SEQ. ID. NO.398), GB-B (SEQUENCE I.D. NO.397, residues 1212-1408) virus and HCV-1 (SEQUENCE I.D. NO.398), andGB-A (SEQUENCE I.D. NO. 390, residues 1252-1449) virus and GB-B(SEQUENCE I.D. NO. 397, residues 1212-1408) virus are 47%, 55% and 43.5%identical, respectively. In addition, over the 100 residue region ofNS5b shown in FIG. 24B, GB-A (SEQUENCE I.D. NO. 390, residues 2644-2739)virus and HCV-1 (SEQUENCE I.D. NO. 398), GB-B (SEQUENCE I.D. NO. 397,residues 2513-1612) virus and HCV-1 (SEQUENCE I.D. NO.398), and GB-A(SEQUENCE I.D. NO. 390, residues 2644-2739) virus and GB-B (SEQUENCEI.D. NO. 397, residues 2599-2698) virus are 36%, 41% and 44% identical,respectively. Lower levels of homology are found in other putativenonstructural genes of GB-A (SEQUENCE I.D. NO. 390) and GB-B (SEQUENCEI.D. NO. 397) when compared to HCV. The overall level of homology of theputative nonstructural proteins of GB-A virus and GB-B virus comparedwith HCV sequences present in GenBank suggests that both GB-A (SEQUENCEI.D. NO. 164) and GB-B (SEQUENCE I.D. NO. 393) are derived from twoseparate members of the Flaviviridae. Flaviviruses contain a singlegenomic RNA molecule which code for one NTP-binding helicase domain andone RNA-dependent RNA polymerase domain. The presence of two contigs,each containing a putative RNA helicase domain and a putativeRNA-dependent RNA polymerase is consistent with the presence of twoHCV-like flaviviruses in the acute phase T-1053 plasma.

Example 10 PCR

In order to determine the sequence relatedness of HGBV to hepatitis Cvirus the following PCR-based experiment was performed. PCR primersbased on the 5′-untranslated region (UTR) sequence of the HCV genome (J.H. Han, PNAS 88:1711-1715 [1991]), which are highly conserved in HCVisolates from a variety of geographic origins (Cha, T.-A., et al., J.Clin. Microbiol. 29:2528-2534 [1991]) were utilized in attempts todetect similar sequences in H205-infected tamarin T-1053 liver RNA.Total cellular RNA was extracted from the liver of infected tamarinT1053 and from the liver of an uninfected tamarin (T-1040) as describedin Example 8A. Thirty micrograms of each RNA sample was reversetranscribed and PCR amplified using a kit available from Perkin-Elmeressentially as described in the manufacturer's instructions. Anantisense primer (primer 1) was used for the reverse transcriptasereaction and comprised bases 249-268 of the HCV 5′-UTR. Primer 1 and aprimer comprising bases 13-46 of the HCV 5′-UTR (primer 2) were thenused for PCR amplification of the intervening sequence. The conditionsused for thermocycling were essentially as described by Cha et al.,supra.

In order to increase the sensitivity of this assay for the detection ofHCV 5′-UTR sequences in H205 infected tamarin T-1053, the above PCRreaction was subjected to a second amplification reacton which utilized“nested” PCR primers. These primers are derived from sequences foundinternal to the sequences of primers 1 and 2 above in the HCV 5′-UTR:Primer 3 comprised sequences from 47-69 and primer 4, an antisenseprimer, comprised bases 188-210 of the HCV 5′-UTR. In this “nested” PCRreaction, PCR products (2 μl out of a total of 100 μl reaction volume)from the first PCR reaction were used as the source of DNA template. Thethermocycling parameters were essentially the same as described aboveexcept that the annealing temperature was 55° C. instead of 60° C. Theresulting PCR products from the second PCR reaction were then analyzedfor the expected DNA products by agarose gel electrophoresis andethidium bromide staining. The expected DNA fragment sizes, based on thesequence of the HCV 5′UTR (Han et al., supra) is 253 bp for the productof the first PCR reaction and 163 bp for the product of the nested PCRreation. PCR products of the anticipated size were obtained in controlexperiments performed using 30 μg of total celluar RNA extracted formthe liver of an HCV infected chimpanzee as described in Example 8A (datanot shown), thus demonstrating that this experimental procedure was ableto detect the 5-UTR of HCV. However, neither of the expected productswere observed on the resulting ethidium bromide stained agarose gel wheneither T-1053 liver RNA or T-1040 liver RNA were used (data not shown).This inability to produce the predicted result may suggest that (i) thesequence of the 5′-UTR of the agent differs significantly from that ofHCV such that the oligonucleotide primers used would not be able toanneal efficiently thereby dissallowing PCR amplification from occurringor (ii) the agent lacks a 5′-UTR. In either case it appears from theseresults that the nucleotide sequence of the agent is significantlydifferent from that of HCV.

In addition, nucleic acids were isolated as in Example 7 from achimpanzee plasma pool obtained during the acute phase of anexperimental infection of HCV (G. Schlauder et al., J. Clin.Microbiology 29:2175-2179 [1991]). RT-PCR was performed as described inExample 7 using clone 16 primers (SEQUENCE I.D. NOS. 93 and 94). Nobands of the expected size for these primers were detected by ethidiumbromide staining or after hybridization to a clone 16 specific probe(data not shown). These results support the unrelatedness of clone 16sequence (SEQUENCE I.D. NO. 26) to HCV.

Example 11 Reactivity of HGBV Infected Serum to Other Hepatits Viruses

Serum specimens were obtained prior to, and after, inoculation with HGBVusing either the H205 inoculum (T-1048, T-1057, T-1061) or the T-1053inoculum (T-1051) and tested for antibodies frequently detectedfollowing exposure to known hepatitis viruses. Specimens were tested forantibodies to hepatitis A virus (using the HAVAB assay, available fromAbbott Laboratories, Abbott Park, Ill.), the core protein of hepatitis Bcore (using the Corzyme® test available from Abbott Laboratories, AbbottPark, Ill.), hepatitis E virus (HEV) (using the HEV EIA,—available fromAbbott Laboratories, Abbott Park, Ill.) and hepatitis C virus (HCV)(utilizing HCV second generation test, available from AbbottLaboratories, Abbott Park, Ill.). These tests were performed accordingto the manufacturer's package inserts.

None of the tamarins tested positive for antibodies to HCV or to HEVeither prior to or after HGBV inoculation (see TABLE 12). Therefore,HGBV infection does not elicit detectable antisera against HCV or HEV.

One of the tamarins (T-1061) was positive for antibodies to HAV prior toand after inoculation with HGBV, suggesting a previous exposure to HAV(TABLE 9, T-1061). However, the three remaining tamarins (T-1048, T-1057and T-1051) show no HAV-specific antibodies after HGBV inoculation.Therefore, HGBV infection does not elicit an anti-HAV response. One ofthe tamarins (T-1048) was negative for antibodies to HBV core both priorto and after inoculation with HGBV. Two of the tamarins (T-1061 andT-1057) were positive prior to inoculation with HGBV. One of thetamarins (T-1051) was borderline positive for antibodies to HBV prior toinoculation, but was negative after inoculation. Based on these data,there is no evidence that infection with the HGBV agent induces animmune response to HBV core. Taken together, these data support that theHGBV agent is a unique viral agent, and is not related to any of theviral agents commonly associated with hepatitis in man.

Example 12

Western Blot Analysis of HGBV Infected Liver

As noted in Examples 1 and 2 above, elevated liver enzyme values arenoted in tamarins inoculated with HGBV. If HGBV is indeed a hepatotropicvirus, it would be expected that viral protein(s) would be produced ininfected liver cells, and that an immune response to those proteinswould be generated. In this example, evidence is presented whichsuggests that a unique protein appears in livers obtained fromHGBV-infected tamarins; this protein appears to be specificallyrecognized via Western blot utilizing tamarin serum obtained in theconvalescent stage following infection with HGBV.

HGBV-infected tamarin livers and various control tamarin and chimpanzeelivers were diced and homogenized in PBS (approximately 1 g liver to 5ml) using a Omni-mixer homogenizer. The resulting suspension wasclarified by centrifugation (10,000×g, 1 hour, 4° C.) and bymicro-filtration through 5 μm, 0.8 μm and 0.45 μm filters. The clarifiedhomogenate was centrifuged under conditions pelleting all components of100S or greater. Pellets (100S liver fractions) were taken up in a smallvolume of buffer and stored at −70° C.

SDS polyacrylamide gel electrophoresis (PAGE) was carried out usingstandard methods and reagents (Laemmli discontinuous gels). 100S liverfractions were diluted 1:20 in a sample buffer containing SDS and2-mercaptoethanol and heated at 95° C. for 5 minutes. The proteins wereelectrophoresed through either 12% acrylamide or 4-15% acrylamide lineargradient gels, 7 cm×8 cm, at 200 volts for 30 to 45 minutes. Proteinswere electro-transferred to nitrocellulose membranes using standardmethods and reagents.

Western blots were developed using standard methods. Briefly, thenitrocellulose membrane was briefly rinsed in TBS/Tween and blockedovernight in TBS/CS (100 mM Tris, 150 mM NaCl, 10 mM EDTA, 0.18%Tween-20, 4.0% calf serum, pH 8.0) at 4° C. The nitrocellulose wasplaced in the Multi-screen apparatus and 600 μl of sera was placed inthe channels and followed with a 2 hour room temperature and anovernight 4° C. incubation. After removing the membrane from theMulti-screen apparatus, it was washed 3 times, 5 minutes each, in 15 mlTBS/Tween (50 mM Tris, 150 mM NaCl, 0.05% Tween-20, pH 8.0). Themembrane was incubated for 1 hour at room temperature in 15 ml goatanti-human:HRPO conjugate (0.2 μg/ml TBS/CS). After washing as before,the membrane was incubated in the TMB enzyme substrate solution, rinsedin water and dried.

Proteins isolated from T-1053 liver at sacrifice (12 days post-GBinoculation) and blotted as described above showed a unique immunogenicprotein with an apparent molecular weight of approximately 50 to 80 kDawhen reacted with T-1057 sera from 5, 6, 7, 9 or 11 weeks post-GBinoculation. The band was not present when reacted with T-1057 serapre-inoculation or 3 weeks post-GB inoculation. This band did not appearin the lanes containing liver proteins obtained from an uninoculatedtamarin (T-1040) when reacted with any of these T-1057 sera. Inaddition, a protein of the same size (50 to 80 kDa) was visible when theT-1053 liver proteins were reacted with other post-GB inoculation sera(T-1048 at 11 weeks post-GB inoculation and T-1051 at 8 weeks post-GBinoculation) but not when they were reacted with pre-inoculation serafrom these same animals.

An additional Western blot experiment was performed to determine if thisimmunoreactive band would be detected in liver tissues from otherGB-inoculated tamarins, or in liver tissues of chimpanzees infectedeither with HCV or HBV. In each case, the nitrocellulose stripscontaining the liver proteins were reacted with a pool of sera fromT-1048 (5, 8, and 16 weeks post-GB inoculation) and T-1051 (8 and 12weeks post-GB inoculation). All 5 sera in the pool were mixed in equalproportion. A reactive protein band of 50-80 kDa was seen with all ofthe tamarin liver samples obtained from GB inoculated tamarins (T-1038,T-1049, and T-1055 obtained at 14 days post-GB inoculation and T-1053obtained at 12 days post-GB inoculation). This immunoreactive band wasnot detected in the liver preparations obtained from T-1040(uninoculated) nor in any of the chimp liver preparations (CHAS-457(pre-HCV inoculation), CHAS-457 (HCV+), CRAIG-454 (HCV+) and MUNA-376(HBV+).

Taken together, these data demonstrate the existence of an immunogenicand antigenic protein with an apparent molecular weight of approximately50 to 80 kDa specifically associated with HGBV-infected tamarin liver.The nature of this HGBV-associated protein (ie. whether it is viralencoded or of host origin) is currently under investigation. Regardlessof the source of the HGBV-associated protein, these result areconsistent with HGBV infection inducing an antibody response to anantigen which is present in HGBV-infected tamarin liver.

Example 13 CKS-Based Expression and Detection of Immunogenic HGBV-A andHGBV-B Polypeptides

A. Cloning of HGBV-A and HGBV-B Sequences

The cloning vectors pJO200, pJO201, and pJO202 allow the fusion ofrecombinant proteins to the CMP-KDO synthetase (CKS) protein. Each ofthese plasmids consists of the plasmid pBR322 with a modified lacpromoter fused to a kdsB gene fragment (encoding the first 239 of theentire 248 amino acids of the E. coli CKS protein), and a syntheticlinker fused to the end of the kdsB gene fragment. The synthetic linkersinclude: multiple restriction sites for insertion of genes,translational stop signals, and the trpA rho-independent transcriptionalterminator. The unique restriction sites in this linker region include,from 5′ to 3′, EcoRI, SacI, KpnI, SmaI, BamHI, XbaI, PstI, SphI, andHindIII. Each plasmid allows for insertion in a different reading framewithin the multiple cloning site. The CKS method of protein synthesis aswell as CKS vectors are disclosed in U.S. Pat. No. 5,124,255, whichenjoys common ownership and is incorporated herein by reference, and theuse of CKS fusion proteins in assay formats and test kits is describedin U.S. Ser. No. 07/903,043, which enjoys common ownership and isincorporated herein by reference.

The HGBV-A and HGBV-B sequences obtained from the walking experimentsdescribed in TABLES 9 and 10 (Example 9) were liberated from theappropriate pT7Blue T-vector clones using restriction enzymes listed inTABLES 13 and 14 (10 units, NEB), and purified from 1% low melting pointagarose gels as described in Example 3B. Plasmids pJO200, pJO201, andpJO202 were digested with the same restriction enzymes (10 units, NEB)and dephosphorylated with bacterial alkaline phosphatase (GIBCO BRL,Grand Island, N.Y.). Each purified HGBV fragment was ligated into thedigested, dephosphorylated pJO200, pJO201, and pJO202 and transformedinto E. coli XL1 Blue as described in Example 3B. Standard miniprepanalyses confirmed the successful construction of the CKS/HGBVexpression vectors.

Two additional PCR products were generated specifically for expression.The 2 products, designated 4.1 and 4.2, were predicted to encode theHGBV-B and HGBV-A core regions, respectively (see FIG. 22). PCR product4.1 was generated using primers coreB-s and coreB-a1 (SEQUENCE I.D. NOS.708 and 709) and PCR product 4.2 was generated using primers coreA-s and2.2.1′ (SEQUENCE I.D. NOS. 710 and 138), as described in Example 9. The4.1 sense and antisense primers had EcoRI and BamHI restriction sites,respectively, designed into the ends. The 4.1 PCR product was digested,gel isolated, and ligated to pJO200, pJO201, and pJO202 as describedabove. The sense primer for the 4.2 PCR product had an EcoRI restrictionsite designed into the end, but the antisense primer did not have arestriction site. Thus, the product was cut with EcoRI, gel isolated,and ligated to pJO200, pJO201, and pJO202 which had been digested withBamHI, end-filled with the Klenow fragment of DNA polymerase and dNTPs,digested with EcoRI, and dephosphorylated with bacterial alkalinephosphatase as described in the art.

B. Expression of HGBV-A and HGBV-B Sequences

E. coli XL1 Blue cultures containing the CKS/HGBV expression vectorswere grown at 37° C. with shaking in media containing 32 gm/L tryptone,20 gm/L yeast extract, 5 gm/L NaCl, pH7.4, plus 100 mg/L ampicillin and3 mM glucose. When the cultures reached an OD600 of between 1.0 and 2.0,IPTG was added to a final concentration of 1 mM to induce expressionfrom the modified lac promoter. Cultures were allowed to grow at 37° C.with shaking for an additional 3 hours, and were then harvested. Thecell pellets were resuspended to an OD600 of 10 in SDS/PAGE loadingbuffer (62.5 mM Tris pH6.8, 2% SDS, 10% glycerol, 5% 2-mercaptoethanol,and 0.1 mg/ml bromophenol blue), and boiled for 5 minutes. Aliquots ofthe prepared whole cell lysates were run on a 10% SDS-polyacrylamidegel, stained in a solution of 0.2% Coomassie blue dye in 40%methanol/10% acetic acid and destained in 16.5% methanol/5% acetic aciduntil a clear background was obtained.

The whole cell lysates were run on a second 10% SDS-polyacrylamide gel,and electrophoretically transferred to nitrocellulose forimmunoblotting. The nitrocellulose sheet containing the transferredproteins was incubated in blocking solution (5% Carnation nonfat drymilk in Tris-buffered saline) for 30 minutes at room temperaturefollowed by incubation for 1 hour at room temperature in goat anti-CKSsera which had been preblocked against E. coli cell lysate then diluted1:1000 in blocking solution. The nitrocellulose sheet was washed twotimes with Tris-buffered saline (TBS), then incubated for 1 hour at roomtemperature with alkaline phosphatase-conjugated rabbit anti-goat IgG,diluted 1:1000 in blocking solution. The nitrocellulose was washed twotimes with TBS and the color was developed in TBS containing nitrobluetetrazolium and 5-bromo-4-chloro-3-indolyl phosphate. The appropriatereading frame for each fragment was identified based on expression of animmunoreactive CKS fusion protein of the correct predicted size, andfurther confirmed by DNA sequencing across the vector-insert junction.

After determining the appropriate reading frame for each of thefragments, samples from cultures containing the appropriate constructswere analyzed by SDS-polyacrylamide gel electrophoresis and Westernblot. FIG. 25A shows 2 Coomassie-stained 10% SDS-polyacrylamide gelscontaining the CKS fusion protein whole cell lysates. Lanes 1 and 16contain molecular weight standards with the sizes in kilodaltons shownon the left. The loading order on gel 1 (HGBV-A samples) is as follows:lane 2, clone 1.17 prior to induction; lanes 3-15, clone 4.2, clone1.17, clone 1.8, clone 1.2, clone 1.18 (SEQUENCE I.D. NO. 390), clone1.19, clone 1.20, clone 1.21, clone 1.22 (SEQUENCE I.D. NO. 390), clone2.12, clone 1.5, clone 1.23, and clone 2.18 respectively, all after 3hours of induction. The loading order on gel 2 (HGBV-B samples) is asfollows: lane 17, clone 4.1 prior to induction; lanes 18-29, clone 4.1,clone 1.15, clone 1.14, clone 2.8, clone 1.13, clone 1.12, clone 2.1,clone 1.7, clone 1.3, clone 1.4, clone 1.16, and clone 2.12respectively, all after 3 hours of induction. These proteins were run on2 additional 10% gels, in the same loading order, and transferred tonitrocellulose as described above. The samples were analyzed by Westernblot using a pool of sera from 2 convalescent tamarins, T-1048 andT-1051, as follows: The nitrocellulose sheets containing the sampleswere incubated for 30 minutes in blocking solution, followed by transferto blocking solution containing 10% E. coli lysate, 6mg/ml XL1-Blue/CKSlysate, and a 1:100 dilution of the pooled convalescent tamarin seradescribed in TABLE 6 (Example 4). After overnight incubation at roomtemperature, the nitrocellulose sheets were washed two times in TBS andthen incubated for 1 hour at room temperature in HRPO-conjugated goatanti-human IgG, diluted 1:500 in blocking solution. The nitrocellulosesheets were washed two times in TBS and the color was developed in TBScontaining 2 mg/ml 4-chloro-1-napthol, 0.02% hydrogen peroxide and 17%methanol. As shown in FIG. 25B, three HGBV-B proteins demonstratedimmunoreactivity with the pooled tamarin sera; CKS fusions of clones1.4, 1.7, and 4.1. Clone 1.7 contains the sequence encoding an HGBV-Bimmunogenic region (SEQUENCE I.D. NO. 610) and clone 1.4 contains thesequence encoding two HGBV-B immunogenic regions (SEQ. ID. NOS. 12, 13and 18), identified by immunoscreening of a cDNA library (Example 4)using the same pool of convalescent tamarin sera.

The samples described in the previous paragraph were also analyzed byWestern blot as above using a 1:100 dilution of convalescent serumobtained approximately three weeks following the onset of acutehepatitis from the surgeon GB. The reactivities of the fusion proteinsfrom HGBV-A and HGBV-B with this serum are indicated in TABLES 13 and14. Only one HGBV-B protein (2.1) showed reactivity with this serum, andthe reactivity was quite weak, while two HGBV-A proteins (1.22 [SEQUENCEI.D. NO. 390] and 2.17) exhibited strong reactivity with this serum.These two HGBV-A proteins overlap by 40 amino acids, so this may reflectreactivity with one epitope or more than one epitope. These two HGBV-Aproteins were chosen for use in ELISA assays as described in Example 16.It is of interest to note that although tamarins infected with theeleventh passage GB material (H205 GB pass 11) demonstrate an immuneresponse to several HGBV-B epitopes but no HGBV-A epitopes, serum fromthe original GB source demonstrates significant reactivity with at leastone HGBV-A epitope. This suggests that HGBV-A may have been thecausative agent of hepatitis in the surgeon GB.

Four additional human sera which had indicated the presence ofantibodies to one or more of the CKS/HGBV-A or CKS/HGBV-B fusionproteins by the 1.4, 1.7, or 2.17 ELISAS (see Examples 15 and 16) werechosen for Western blot analysis. Three of these sera (G1-41, G1-14 andG1-31) are from the West African “at risk” population and the fourth(341C) is from a nonA-E hepatitis (Egypt) sample (see Example 15 fordetailed description of these populations). Additional 10%SDS-polyacrylamide gels containing the whole cell lysates from some ofthe CKS fusion proteins discussed above were run and transferred tonitrocellulose as described previously. Each of these blots waspreblocked as described, then incubated overnight with one of the humanserum sample diluted 1:100 in blocking buffer containing 10% E. colilysate and 6mg/ml XL1-Blue/CKS lysate. The blots were washed two timesin TBS, then reacted with HRPO-conjugated goat anti-human IgG anddeveloped as indicated above.

The CKS/HGBV-B proteins were analyzed with two of these sera, G1-41 andG1-14, and the reactivities are indicated in TABLE 13. In addition tothe three proteins which showed reactivity with the tamarin sera, twoadditional proteins (1.16 and 2.1) showed reactivity with one or theother of the two human sera. The CKS/HGBV-A proteins were analyzed withall four of these human sera and the reactivities are indicated in TABLE14. In addition to the two proteins which showed reactivity with GBserum, three additional proteins (1.5, 1.18, and 1.19) showed reactivitywith one or more of the human sera. Two of these (1.5 and 1.18) werechosen for use in ELISA assays as described in Example 16. It is ofparticular interest to note that the G1-31 serum, which shows reactivityby Western blot and/or ELISA (Examples 15 and 16) with two HGBV-Aproteins (1.18 and 2.17) and one HGBV-B protein (1.7), is the serum fromwhich the GB-C sequence (SEQUENCE I.D. No. 673, residues 2274-2640) wasisolated (Example 17).

TABLE 13 HGBV-B Samples Reactivity Reactivity Reactivity with with withT1048 + Reactiv- human human PCR Restriction T1051 ity with G1-41 G1-14product^(a) digest^(b) sera GB sera sera sera 1.3 EcoRI, PstI − − − −1.4 EcoRI, XbaI + − + + 1.7 EcoRI, HindIII + − + − 1.12 KpnI, PstI − − −− 1.13 EcoRI, XbaI − − − − 1.14 BamHI, HindIII − − − − 1.15 EcoRI, PstI− − − − 1.16 EcoRI, XbaI − − + − 2.1 EcoRI, HindIII − +/− − + 2.8 EcoRI,XbaI − − − − 2.12 KpnI, PstI − − − − 4.1 EcoRI, BamHI + − − − ^(a)PCRproduct is as indicated in TABLE 9, TABLE 10, or Example 13.^(b)Restriction digests used to liberate the PCR fragment from pT7BlueT-vector or for direct digestion of 4.1 PCR product.

Example 14 Epitope Mapping of Immunoreactive HGBV-A and HGBV-B Proteins

A. Epitope Mapping of HGBV-B Protein 1.7

Overlapping subclones within the HGBV-B immunogenic protein 1.7 weregenerated by RT-PCR from T1053 serum as described in Example 7 in orderto determine the location of the immunogenic region or regions. Each PCRprimer had six extra bases on the 5′ end to facilitate restrictionenzyme digestion, followed by either an EcoRI site (sense primers) or aHindIII site (antisense primers). In addition, each antisense primercontained a stop codon just after the coding region. After digestion,each fragment was cloned into EcoRI/HindIII-digested pJO201 as describedin Example 13. The CKS fusion proteins were expressed and analyzed byWestern blot with tamarin T1048/T1051 sera as described in Example 13.Five overlapping clones, designated 1.7-1 through 1.7-5, were generated.The clones encoded regions of the 1.7 protein ranging in size from 104to 110 amino acids. The PCR primers used to generate each clone, thesizes of the encoded polypeptides, the location within the 1.7 sequenceand the reactivity with tamarin T1048/T1051 sera are shown in TABLE 15.Two further overlapping clones were generated which encompassed theimmunogenic region (SEQUENCE I.D. NO. 678) identified by immunoscreeningof a cDNA library (Example 4). Each of these clones, designated 1.7-6and 1.7-7, encoded polypeptides of 75 amino acids. The PCR primers,sizes of encoded polypeptides, location within the 1.7 sequence andreactivity with tamarin T1048/T1051 sera are shown in TABLE 15. Twoimmunogenic regions were identified within the 507 amino acid long 1.7protein; one near the N-terminus within residues 1-105, and another nearthe middle of the protein, encompassing residues 185 to 410. It remainsto be determined whether there is a single epitope or multiple epitopeswithin each of these regions.

B. Epitope Mapping of HGBV-B Protein 1.4

Overlapping subclones within the HGBV-B immunogenic protein 1.4 weregenerated by RT-PCR from T1053 serum as above in order to determine thelocation of the immunoreactive region or regions. Each PCR primer hadsix extra bases on the 5′ end to facilitate restriction enzymedigestion, followed by either an EcoRI site (sense primers) or a BamHIsite (antisense primers). In addition, each antisense primer contained astop codon just after the coding region. After digestion, each fragmentwas cloned into EcoRI/BamHI-digested pJO201 as described in Example 13.The CKS fusion proteins were expressed and analyzed by Western blot withtamarin T1048/T1051 sera as described in Example 13. Four overlappingclones, designated 1.4-1 through 1.4-4, were generated. The clonesencoded regions of the 1.4 protein ranging in size from 137 to 138 aminoacids. The PCR primers used to generate each clone, the sizes of theencoded polypeptides, the location within the 1.4 sequence and thereactivity with tamarin T1048/T1051 sera are shown in TABLE 15. Twofurther overlapping clones were generated which encompassed animmunogenic region identified by immunoscreening of a cDNA library(Example 4). Each of these clones, designated 1.4-5 and 1.4-6, encodedpolypeptides of 75 amino acids. The PCR primers, sizes of encodedpolypeptides, location within the 1.4 sequence and reactivity withtamarin T1048/T1051 sera are shown in TABLE 15. A 265 amino acidsequence was identified as being the immunogenic region within the 522amino acid long 1.4 protein, encompassing residues 129 to 393. It islikely that there are at least two epitopes within this region, sincelibrary immunoscreening (Example 4) identified two immunogenicnon-contiguous clones within this sequence.

C. Epitope Mapping of HGBV-A Proteins 1.22 (SEQUENCE I.D. NO. 390) and2.17

The HGBV-A proteins 1.22 (SEQUENCE I.D. NO. 390 and 2.17 (SEQUENCE I.D.NO. 613) both showed immunoreactivity with GB serum by Western blot(Example 13). Since these two proteins overlap by 40 amino acids, theobserved immunoreactivity may have resulted from the presence of oneepitope or more than one epitope. The complete 1.22/2.17 sequence is 641amino acids long. Overlapping subclones within this region weregenerated by RT-PCR from T1053 serum as above in order to determine thelocation of the immunogenic region or regions. Each PCR primer had sixextra bases on the 5′ end to facilitate restriction enzyme digestion,followed by either an EcoRI site (sense primers) or a BamHI site(antisense primers) for 1.22/2.17-2 through 1.22/2.17-6. However, sinceclone 1.22/2.17-1 had an internal EcoRI site, a BamHI site was used inthe sense primer and a HindIII site was used in the antisense primer. Inaddition, each antisense primer contained a stop codon just after thecoding region. After digestion, each fragment was cloned intoEcoRI/BamHI-digested (or BamHI/HindIII-digested for 1.22/2.17-1) pJO201as described in Example 13. The CKS fusion proteins were expressed andanalyzed by Western blot with GB serum as described in Example 13. Theclones encoded regions of 1.22/2.17 ranging in size from 115 to 116amino acids. The PCR primers used to generate each clone, the sizes ofthe encoded polypeptides, the location within the HGBV-A polypeptidesequence and the reactivity with GB serum are shown in TABLE 15. Theimmunogenic region was narrowed down to a 220 amino acid long region inthe middle of the 1.22/2.17 protein. This encompassed the 40 amino acidregion of overlap between 1.22 and 2.17, and thus the immunoreactivityseen with the two proteins individually may have been due to a sharedepitope or to multiple epitopes.

TABLE 15 SIZE OF RESIDUES ENCODED PRIMER T1048/T1051 IN SEQ I.D. CLONEPOLYPEPTIDE SET REACTIVITY NO. 120 1.7-1 105 aa SEQ ID #615/SEQID #616 + 1-105 1.7-2 109 aa SEQ ID #617/SEQID #618 −  98-206 1.7-3 110 aa SEQ ID#619/SEQID #620 + 199-308 1.7-4 110 aa SEQ ID #621/SEQID #622 +/−301-410 1.7-5 104 aa SEQ ID #623/SEQID #624 − 403-507 1.7-6  75 aa SEQID #625/SEQID #626 + 185-259 1.7-7  75 aa SEQ ID #627/SEQID #628 +251-325 SIZE OF RESIDUES ENCODED PRIMER T1048/T1051 IN SEQ I.D. CLONEPOLYPEPTIDE SET REACTIVITY NO. 119 1.4-1 137 aa SEQ ID #629/SEQID #630 − 1-137 1.4-2 137 aa SEQ ID #631/SEQID #632 + 129-265 1.4-3 137 aa SEQ ID#633/SEQID #634 + 257-393 1.4-4 138 aa SEQ ID #635/SEQID #636 − 385-5221.4-5  75 aa SEQ ID #637/SEQID #638 + 138-212 1.4-6  75 aa SEQ ID#639/SEQID #640 + 204-278 SIZE OF RESIDUES ENCODED PRIMER GB SERUM INSEQ I.D. CLONE POLYPEPTIDE SET REACTIVITY NO. 390 1.22/2.17-1 115 aa SEQID #641/SEQID #642 − 1862-1976 1.22/2.17-2 115 aa SEQ ID #643/SEQID #644− 1967-2081 1.22/2.17-3 115 aa SEQ ID #645/SEQID #646 + 2072-21861.22/2.17-4 115 aa SEQ ID #647/SEQID #648 + 2177-2291 1.22/2.17-5 115 aaSEQ ID #649/SEQID #650 − 2282-2396 1.22/2.17-6 116 aa SEQ ID #651/SEQID#652 − 2387-2505

Example 15 Serological Studies HGBV-B

A. Recombinant Protein Purification Protocol

Bacterial cell cultures expressing the CKS fusion proteins were frozenand stored at −70° C. The bacterial cells from each of the threeconstructs were thawed and disrupted by treating with lysozyme andDNAse, followed by sonication in the presence of phenylmethanesulfonylfluoride and other protease inhibitors to produce mixtures of theindividual recombinant antigen and E. coli proteins. Individually foreach of the three cultures, the insoluble recombinant antigen wasconcentrated by centrifugation and subjected to a series of sequentialwashes to eliminate the majority of non-recombinant E. coli proteins.The washes used in this protocol included distilled water, 5% TritonX-100 and 50 mM Tris (pH 8.5). The resulting pellets were solubilized inthe presence of sodium dodecyl sulfate (SDS). After determining proteinconcentration, 2-mercaptoethanol was added and the mixtures weresubjected to gel filtration column chromatography, with Sephacryl S300resin used to size and separate the various proteins. Fractions werecollected and analyzed by SDS-polyacrylamide gel electrophoresis(SDS-PAGE) The electrophoretically separated proteins were then stainedwith Coomassie Brilliant Blue R250 and examined for the presence of aprotein having a molecular weight of approximately 75 kD(CKS-1.7/SEQUENCE I.D. NO. 610), 80 kD (CKS-1.4/SEQUENCE I.D. NO. 611),42 kD (CKS-4.1/SEQUENCE I.D. NO. 612). Fractions containing the proteinof interest were pooled and re-examined by SDS-PAGE.

The immunogenicity and structural integrity of the pooled fractionscontaining the purified antigen were determined by immunoblot followingelectrotransfer to nitrocellulose as described in Example 13. In theabsence of a qualified positive control, the recombinant proteins wereidentified by their reactivity with a monoclonal antibody directedagainst the CKS portion of each fusion protein. When the CKS-1.7 protein(SEQUENCE I.D. NO. 610) was examined by Western blot, using the anti-CKSmonoclonal antibody to detect the recombinant antigen, a single band atapproximately 75 kD was observed. This corresponds to the expected sizeof the CKS-1.7 protein (SEQUENCE I.D. NO. 610). For the CKS-1.4 protein(SEQUENCE I.D. NO. 611), the anti-CKS monoclonal antibody detects aquadruplet banding pattern between 60 and 70 kD. These observed bandsare smaller than the expected size of the full length protein andprobably represent truncation products. When the CKS-4.1 protein(SEQUENCE I.D. NO. 52) was examined by Western blot, the anti-CKSmonoclonal antibody detected the recombinant antigen as a single band atapproximately 42 kD. This corresponds to the expected size of theCKS-4.1 protein (SEQUENCE I.D. NO. 612).

B. Polystyrene Bead Coating Procedure

The proteins were dialyzed and evaluated for their antigenicity onpolystyrene coated beads as described below. Separate enzyme-linkedimmunosorbent assays (ELISA's) were developed for detecting antibodiesto HGBV using each of the three purified HGBV recombinant proteins(CKS-1.7 (SEQUENCE I.D. NO. 610); CKS-1.4 (SEQUENCE I.D. NO. 611); andthe CKS-4.1 protein (SEQUENCE I.D. NO. 612). The ELISA's developed withthese proteins are referred to as the 1.7 ELISA (utilizing the CKS-1.7(SEQUENCE I.D. NO. 610) recombinant protein), the 1.4 ELISA (utilizingthe CKS-1.4 (SEQUENCE I.D. NO. 611) recombinant protein), the 4.1 ELISA(utilizing the CKS-4.1 [SEQUENCE I.D. NO. 612]) recombinant protein. Inthe first study, one-quarter inch polystyrene beads were coated withvarious concentrations with each of the purified proteins (approximately60 beads per lot) and evaluated in an ELISA test (described below) usingserum from an uninoculated tamarin as a negative control andconvalescent sera from an inoculated tamarin as a positive control.Additional controls included the a pool of human serum from individualstesting negative for various hepatitis viruses. An additional positivecontrol consisted of monoclonal antibodies to the CKS protein to monitorthe efficiency of bead coating. The bead coating conditions providingthe highest ratio of positive control signal to negative control signalwere selected for scaling up the bead coating process. For each of thefour ELISA's at least two lots of 1,000 beads were produced and utilizedfor serological studies.

Briefly, polystyrene beads were coated with the purified proteins byadding the washed beads to a scintillation vial and immersing the beads(approximately 0.233 ml per bead) in a buffered solution containing therecombinant antigen. Several different concentrations of each of therecombinant antigens were evaluated along with several different buffersprepared at pHs ranging from pH 5.0 to pH 9.5. The vials were thenplaced on a rotating device in a 40° C. incubator for 2 hours afterwhich the fluids were aspirated and the beads were washed three times inphosphate buffered saline (PBS), pH 6.8. The beads were then treatedwith 0.1% Triton X-100 for 1 hour at 40° C. and washed three times inPBS. Next, the beads were overcoated with 5% bovine serum albumin andincubated at 40° C. for 1 hour with agitation. After additional washingsteps with PBS, the beads were overcoated with 5% sucrose for 20 minutesat room temperature and the fluids were aspirated. Finally, the beadswere air dried and then utilized for developing ELISA's for detection ofantibodies to HGBV.

C. ELISA Protocol for Detection of Antibodies to HGBV

An indirect assay format was utilized for the ELISA's. Briefly, sera orplasma was diluted in specimen diluent and reacted with the antigencoated solid phase. After a washing step, the beads were reacted withhorseradish-peroxidase (HRPO) labeled antibodies directed against humanimmunoglobulins to detect tamarin or human antibodies bound to the solidphase. Specimens which produced signals above a cutoff value wereconsidered reactive. Additional details pertaining to the ELISA's aredescribed below.

The format for the ELISA's entails contacting the antigen-coated solidphase with tamarin serum pre-diluted in specimen diluent (bufferedsolution containing animal sera and non-ionic detergents). This specimendiluent was formulated to reduce background signals obtained fromnon-specific binding of immunoglobulins to the solid phase whileenhancing the binding of specific antibodies to the antigen-coated solidphase. Specifically, 10 μl of tamarin serum was diluted in 150 μl ofspecimen diluent and vortexed. Ten microliters of this pre-dilutedspecimen was then added to the well of a reaction tray, followed by theaddition of 200 μl of specimen diluent and an antigen coated polystyrenebead. The reaction tray was then incubated in a Dynamic Incubator(Abbott Laboratories) set for constant agitation at room temperature.After a 1 hour incubation, the fluids were aspirated, and the wellscontaining the beads were washed three times in distilled water (5 mlper wash). Next, 200 μl of HRPO-labeled goat anti-human immunoglobulinsdiluted in a conjugate diluent (buffered solution containing animal seraand non-ionic detergents) was added to each well and the reaction traywas incubated again as above for 1 hour. The fluids were aspirated andthe wells containing the beads were washed three times in distilledwater as above. The beads containing antigen and bound immunoglobulinswere removed from the wells, each was placed in a test tube and reactedwith 300 μL of a solution of 0.3% o-phenylenediamine-2 HCl in 0.1 Mcitrate buffer (pH 5.5) with 0.02% H₂O₂. After 30 minutes at roomtemperature, the reaction was terminated by the addition of 1 N H2SO₄.The absorbance at 492 nm was read on a spectrophotometer. The colorproduced was directly proportional to the amount of antibody present inthe test sample.

For each group of specimens, a preliminary cutoff value was set toseparate those specimens which presumably contain antibodies to the HGBVepitope from those which did not.

D. Detection of HGBV Derived RNA in Serum from Infected Individuals

In order to correlate serological data obtained for 1.7 and 1.4 ELISA'swith the presence of HGBV RNA in tamarin serum or in human serum/plasma,RT-PCR was performed as described in Example 7 of U.S. Ser. No.08/283,314, previously incorporated herein by reference utilizingoligonucleotides derived from HGBV cloned sequences, at a finalconcentration of 0.5 μM for clone 4 (as described in Example 7) derivedfrom the HGBV-B genome and for clone 16, derived from the HGBV-A genome.

E. Tamarin Serological Profiles

Serum was obtained from tamarins housed at LEMSIP on a weekly basis andtested for liver enzyme levels; the remaining volume from thesespecimens was sent to Abbott Laboratories for further studies.

1. ELISA Results on Tamarins (Initial Infectivity Studies)

Four tamarins (T-1053, T-1048, T-1057 and T-1061) were inoculated withGB serum (designated as H205 GB passage 11). Elevated liver enzymes werenoted in Tamarin T-1053 during the first week post-inoculation (PI):this tamarin was euthanized on day 12 PI. Tamarins T-1048, T-1057 andT-1061 exhibited elevated liver enzyme values within two weeks followingtheir inoculation; these elevated values persisted until 8-9 weeks PI(FIGS. 2-4) before returning to pre-inoculation levels. On week 14 PI,these three tamarins were re-challenged with 0.10 ml of neat serumobtained from tamarin T-1053 (which was shown to be infectious—Example2).

Sera from three convalescing tamarins (T-1048, T-1057 and T-1061) weretested for antibodies to the CKS-1.7 (SEQUENCE I.D. NO. 610) recombinantprotein, the CKS-1.4 (SEQUENCE I.D. NO. 611) recombinant protein, andthe CKS 4.1 (SEQUENCE I.D. NO. 612) recombinant protein, using separateELISA's (FIGS. 3, 4 and 5). Specific antibodies to 1.7 (SEQUENCE I.D.NO. 610), 1.4 (SEQUENCE I.D. NO. 611), 4.1 (SEQUENCE I.D. NO. 612, or1.5 (SEQUENCE I.D. NO.614) recombinant proteins were not detected in anyof the pre-inoculation specimens.

As shown in FIG. 26, specific antibodies were detected in T-1048 serawith the 1.7 and 1.4 ELISA's on days 56-84 but not on days 97 and 137PI. Specific antibodies were not detected in T-1048 sera tested with the4.1 ELISA. As shown in FIG. 27, antibodies to the 1.7 protein (SEQUENCEI.D. NO. 610) were detected in T-1057 serum at 56 and 63 days PI, butnot after 63 days PI. Antibodies to the 4.1 protein (SEQUENCE I.D.NO.612) were detected on days 28-63 PI but not on days 84-97 PI. Asnoted above, tamarins were challenged with a second dose of the H205inoculum on day 97 PI. Specific antibodies to the 4.1 protein (SEQUENCEI.D. NO. 612) were detected on days 112 and 126 PI, suggesting ananamnestic response to the inoculum. No antibody reactivity was notedfor the 1.4 recombinant protein (SEQUENCE I.D. NO. 611).

Specific antibodies to the recombinant 1.4 protein (SEQUENCE I.D. NO.611) were detected in the serum of tamarin T-1061 between 84 and 112days PI, but were not detected after 126 days PI. As shown in FIG. 28,Tamarin T-1061 sera were negative for antibodies to the 1.7 protein(SEQUENCE I.D. NO. 610) and to the 4.1 protein (SEQUENCE I.D. NO. 612)for 350 days PI.

2. PCR Results on Tamarins (Initial Infectivity Studies)

Selected sera obtained from tamarins T-1048 and T-1057 were tested forHGBV RNA via RT-PCR using primers from clone 4 as described in Example7) and from clone 16 as described in Example 7.

HGBV RNA was not detected via RT-PCR with either set of primers in theserum obtained 10 and 17 days prior to inoculation (T-1048) as shown inFIG. 26, or 17, 37 and 59 days prior to inoculation (T-1057), as shownin FIG. 27. For T-1048, HGBV RNA was detected via RT-PCR using primersfrom clone 4 on fifteen of seventeen different sera obtained between7-137 days PI. HGBV RNA was not detected via RT-PCR using primers fromclone 16 in any of the 10 sera obtained on days 7-97 PI. After thechallenge with T-1053 plasma, four of five sera obtained between 8 and40 days after the challenge were positive for clone 16. For T-1057,positive RT-PCR results were obtained on four sera obtained on days 7-28PI, using primers from clone 4, as shown in FIG. 27. RT-PCR performed onspecimens drawn beyond day 28 PI were negative for clone 4, except forday 287 which showed a weak hybridization signal. Neither of the sixspecimens obtained from T-1057 on day 7-97 PI were positive via RT-PCRusing primers from clone 16. However, sera obtained between 8-85 daysafter the T-1053 challenge were positive using primers from clone 16.

3. ELISA Results on Tamarins (Titration/Transmissibility Studies)

As described in Example 2, serum from tamarin T-1053 was inoculated intofour tamarins. Three of these four tamarins were euthanized during theacute stage of the disease (between days 12 and 14 PI). The RT-PCRresults obtained on these three tamarins are described below. Thesurviving tamarin (T-1051) first developed elevated liver enzyme valuesby day 14 PI and these values persisted for at least 8 weeks PI.Specimens from tamarin T-1051 were tested in the 1.7 and 1.4 ELISA's;the results are shown in FIG. 29. Specific antibodies were not detectedin the pre-inoculation serum nor in serum drawn in the first 41 days PI.However, an antibody response was noted against the 1.4 protein(SEQUENCE I.D. NO. 611), and the 1.7 protein (SEQUENCE I.D. NO. 610)between 49 and 113 days PI and the 4.1 protein (SEQUENCE I.D. NO. 612)between 28 and 105 days PI. The tamarin was euthanized during the 113thday PI.

Tamarin (T-1034) was previously inoculated with 0.1 ml of potentiallyinfectious serum obtained from a patient (original GB source) who wasrecovering from a recent hepatitis infection as described in Example 1and in TABLE 4. No elevations in liver enzyme values were noted inT-1034 for nearly 10 weeks after inoculation. For this reason, it wasdecided that tamarin T-1034 could be used in an additional study.Tamarin T-1034 was inoculated with a preparation of HGBV prepared asdescribed in Example 4 ?? from a pool of serum obtained from threetamarins (T-1055, T-1038 and T-1049) previously inoculated with serumfrom tamarin T-1053.

These three tamarins (T-1055, T-1038 and T-1049) were inoculated withserum prepared from tamarin T-1053 as described in Example 2. Elevatedliver enzyme values were noted in all 3 tamarins by day 11 PI. TamarinT-1055 was sacrificed on day 12 PI: tamarins T-1038 and T-1049 weresacrificed on day 14 PI. Serum from these tamarins was pooled, clarifiedand filtered. Tamarin T-1034 was inoculated with 0.25 ml of a 10⁻⁶dilution (prepared in normal tamarin serum) of this filtered material.

Elevated ALT liver enzyme values were first noted in T-1034 at 2 weeksPI, and remained elevated for the next 7 weeks, finally normalizing byweek 10 PI. As demonstrated in FIG. 30, a specific antibody response tothe 1.4 (SEQUENCE I.D. NO. 22) recombinant protein was first detected onday 49 PI and continued to be detected on days 56-118 PI. The antibodyresponse to the 4.1 (SEQUENCE I.D. NO. 52) recombinant protein was firstdetected on day 49 PI and continued to be detected between days 56-77PI, but was not detected on between days 84-118 PI. The antibodyresponse to the 1.7 (SEQUENCE I.D. NO. 610) recombinant protein wasfirst detected on day 56 PI and continued to be detected between days63-118 PI. The tamarin was sacrificed on day 118 PI.

As described in Example 2, tamarin T-1044 was inoculated with serumobtained from T-1057 that had been obtained 7 days after the H205inoculation. This inoculum was positive only for sequences detected withclone 4 primers. The inoculum was negative by RT-PCR with clone 16primers. Mild elevations in ALT levels above the cutoff were observedfrom days 14-63 PI. As demonstrated previously, a specific antibodyresponse to the 1.7 (SEQUENCE I.D. NO. 610) recombinant protein wasdetected between 63-84 days PI. No antibody response to the 4.1(SEQUENCE I.D. NO. 612) recombinant protein or to the 1.4 (SEQUENCE I.D.NO. 611) recombinant protein was detected. The tamarin was sacrificed on161 days PI.

4. PCR Results on Tamarins (Titration/Transmissibilty Studies)

Sera obtained from T-1049 and T-1055 during the 8th week prior toinoculation and T-1038 on the day of inoculation, were negative byRT-PCR for sequences to clone 16 (SEQUENCE I.D. NO. 26) and clone 4(SEQUENCE I.D. NO. 21). Tamarins T-1049 and T-1055 were positive forclone 4 sequences (SEQUENCE I.D. NO. 21) by RT-PCR 1 week afterinoculation (clone 16 PCR was not done). Prior to the day of sacrifice,T-1049 (14 days PI) as well as T-1055 (11 days PI) were positive byRT-PCR for both clone 4 (SEQUENCE I.D. NO. 21) and clone 16 sequences(SEQUENCE I.D. NO. 26). Tamarin T-1038 was positive with both sets ofprimers on the day of sacrifice (14 days PI).

As seen in FIG. 30, T-1034 was positive by RT-PCR for sequences detectedwith clone 4 primers on the first serum sample obtained afterinoculation (7 days PI) and remained positive to day 70 PI. A sampleobtained on day 112 PI was negative. All of these samples were negativeby RT-PCR with clone 16 primers. Samples obtained 70 and 101 days priorto inoculation were negative with both sets of primers.

As can be seen in FIG. 29 for tamarin T-1051, HGBV RNA was not detectedwith either set of primers (from clones 4 and 16 as described above) inthe serum specimen obtained 8 weeks prior to inoculation. HGBV RNA wasdetected by RT-PCR using primers from clone 4 on six sera obtainedbetween days 7-69 PI, but not on days 77, 84, 91, or 105 PI. HGBV RNAwas detected by RT-PCR using primers from clone 16 on nine samplesobtained after inoculation.

As seen in FIG. 7, T-1044 was positive by RT-PCR for sequences detectedwith clone 4 primers on the first serum sample obtained afterinoculation (7 days PI) and remained positive to day 63 PI. Samplesobtained between days 77-119 were negative. All of these samples werenegative by RT-PCR with clone 16 primers. A sample obtained 42 daysprior to inoculation was negative for both sets of primers.

Tamarins T-1047 and T-1056 were inoculated with T-1044 serum obtained 14days PI. Nine samples obtained between 7-64 days PI from both of theseanimals were positive by RT-PCR with clone 4 primers (SEQUENCE I.D. NOS.8 and 9) but negative with clone 16 primers.

Tamarin T-1058 was inoculated with neat T-1057 serum obtained 22 daysafter the challenge with T-1053 serum. This inoculum was positive forsequences detected with clone 16 primers but negative with clone 4primers. Serum samples obtained from this animal were tested withprimers derived from GBV-sequences [clone 16, clone 2 clone 10 and clone18)] and GB-B sequences [clone 4 and clone 50]. A sample obtained 9 daysprior to inoculation was negative with all primer sets. A sampleobtained 14 days PI was positive only with clone 10 and 18 primers. Asample obtained 21 days PI was positive only with clone 16, 10 and 18primers. A sample obtained 28 days PI was positive only with clone 18primers. A sample obtained 35 days PI was positive only with clone 2, 16(and 18 primers. A sample obtained 41 days PI was positive only withclone 16 and 18 primers. All samples tested were negative with primersfrom clone 4 and clone 50.

5. Summary of Serological Studies in Tamarins

Five tamarins were inoculated with various preparations of HGBV anddeveloped elevated liver enzyme values by two weeks PI. These elevationspersisted for the next six to eight weeks. A specific antibody responseto one or more HGBV recombinant antigens, 1.7, 1.4, and 4.1 was noted inall five tamarins. In all cases, the antibodies were first detected bysix to ten weeks PI, and persisted for two to seven or more weeks. Ingeneral, the antibody levels peaked and then declined rapidly over thenext several weeks. It is observed that the antibodies become detectableshortly after the liver enzyme values returned to normal levels,suggesting that the generation of antibodies may play a role in clearingthe viral infection.

6. Summary of PCR Studies on Tamarins

The results of the genomic walking experiments suggest that clone 4(SEQUENCE I.D. NO.21) and clone 16 (SEQUENCE I.D. NO. 26) reside onseparate RNA molecules. We previously provided arguments that supportedthe idea that there are two distinct viral genomes, one comprised partlyof clone 4 (SEQUENCE I.D. NO.21) and one comprised partly of clone 16(SEQUENCE I.D. NO. 26). The observation that some animals are positivewith primers from clone 4 and not with primers from clone 16 supportedthe existence of two distinct viral genomes. However, it can also beargued that the inability to detect clone 16 (SEQUENCE I.D. NO. 26)sequence in some of the infected tamarins may reflect a lower limit ofsensitivity of the clone 16 primer set relative to the clone 4 primerset. If this latter possibility was the case, then a tamarin positivefor both primer sets should exhibit a difference in sensitivity withthese two primer sets. In order to support the explanation that theseresults are explained by the existence of two separate viruses, and notdifferences in sensitivities of these two primer sets, PCR was performedon a dilution series of cDNA from tamarins T-1057 and T1053. T-1057serum was positive at 5×10⁻³ but negative at 5×10⁻⁴ ul serum equivalentswith clone 4 primers. As much as 20 ul of T-1057 serum was used forRT-PCR with clone 16 primers with negative results. If this differencewas due to the relative sensitivity of the two primer sets (clone 4 vs.clone 16), one would expect that other specimens would also show a 4000fold higher endpoint dilution when tested by PCR. However, cDNA derivedfrom T-1053 serum was found to be positive at 2.5×10⁻⁴ but negative at2.5×10⁻⁵ ul serum equivalents for both clone 4 (SEQUENCE I.D. NO.21) andclone 16 (SEQUENCE I.D. NO. 26) sequences. These observations aretherefore not consistent with a difference in sensitivity of primer setsbut are consistent with the existence of contig B-clone 4 (SEQUENCE I.D.NO.21) and contig A-clone 16 (SEQUENCE I.D. NO. 26) sequences onseparate viral genomes of roughly equal titer in T-1053 but differing intiter by at least 4000 fold in T-1057. This data is therefore consistentwith the existence of two separate viruses which may have differentrelative endpoint titers in different specimens.

The observation that HGBV-B viremia alone was sufficient to causeelevations in liver enzyme levels and that no elevations were observedduring a GBV-A-only viremic stage, indicated that HGBV-B was theprobable causative agent for hepatitis in these tamarins. The immuneresponse to the HGBV-B antigens appeared to be for a short duration, atmost 150 days PI. One explanation could be that the selection ofepitopes used in these ELISAs was not from the dominant epitopes towhich the immune response is generated. Another explanation could bethat in tamarins the hepatic challenge may not be significant enough tonecessitate a long-lived response. This is consistent with histologicalevidence from animals that were sacrificed during the acute phase of thedisease or had died of natural causes some time after the acute phasewhich showed that hepatic inflammation ranged from mild to notsignificant (results not shown).

Five of six animals described in this study resolved viremia of HGBV-Bby 112 days PI. In contrast, Tamarin T-1048 remained viremic for 136days and was found to be viremic at the time of death (137 days PI). Ofthe four animals that were positive for GBV-A sequence, three showedresolution by 77 days after the first appearance of GBV-A sequence. Incontrast, tamarin T-1061 was viremic for 245 days up to the time theanimal was sacrificed. In addition, tamarin T-1051 was viremic up to thetime of sacrifice (day 113 PI), however, it is unclear if thispersistent viremia is due to the initial inoculation with T-1053 plasmaor a result of the subsequent challenge with additional T-1053 plasma 69days later.

The average peak ALT value for the six animals positive for both HGBV-Aand HGBV-B was higher than the average value for the four HGBV-B-onlyanimals. In addition, the peak value occurred, on average, earlier inanimals positive for GBV-A and GBV-B than for animals positive only forGBV-B. These results suggest that the intensity of the hepatitis may berelated to the presence of both agents at significant levels. Theobservation from the additional passage of GBV-B into tamarins T-1047and T-1056 that minimal elevation in liver enzymes occurred with GBV-Bviremia supports this assumption that both agents may be necessary formajor elevations in ALT levels to occur in tamarins. In addition to thepassage of HGBV-B alone, initial results from the inoculation of T-1058with HGBV-A inoculum suggest thatH GBV-A can be transmitted independentof any detectable HGBV-B as indicated by the absence of any detectableGB-B sequences with clone 4 and clone 50 primers.

F. Experimental Protocol.for Demonstrating Exposure to HGBV in HumanPopulations

Specimens were obtained from various human populations and tested forantibodies to HGBV utilizing three separate ELISA's utilizingrecombinant proteins derived from HGBV-B. The 1.7 ELISA utilized theCKS-1.7 recombinant protein (SEQUENCE I.D. NO.610) coated onto the solidphase; the 1.4 ELISA utilized the CKS-1.4 recombinant proteins (SEQUENCEI.D. NO.611) coated on the solid phase and the 4.1 ELISA utilized the4.1 recombinant protein (SEQUENCE I.D. NO.612) coated on the solid phaseas described in Example 15.B. As also noted in Example 15.E, tamarinsinoculated with HGBV produce a specific, but short-lived antibodyresponse to these proteins. In view of the transient nature of thisdetectable immune response, a negative result in human populations wouldnot necessarily exclude previous exposure to HGBV.

The objective of the serological studies conducted with human specimenswas two-fold. First, the seroprevalence of antibodies to the currentHGBV recombinant antigens in various human populations was to bedetermined. These studies included testing (1) populations considered at“low risk” for exposure to HGBV (e.g. healthy volunteer blood donors inU.S.); (2) populations considered to be “at risk” for exposure to HGBV(e.g. specimens obtained from intravenous drug users and hemophiliacsare frequently seropositive for parenterally transmitted hepatitisviruses (HBV and HCV); specimens obtained from individuals residing indeveloping nations are frequently seropositive for entericallytransmitted viruses (HAV and HEV); (3) panels of specimens obtained fromindividuals with “non-A-E hepatitis” that is not associated withexposure to known hepatitis viruses (HAV, HBV, HCV, HDV or HEV) or toother viruses associated with hepatitis such as cytomegalovirus (CMV) orEpstein-Barr Virus (EBV). In some cases, members of the panels under thegeneral heading of non A-E hepatitis were not tested for antibodies toHEV. Therefore, all specimens in the non A-E group which were reactivewith the 1.7, 1.4 or 4.1 ELISA's were retested with an HEV ELISA assay(available from Abbott Laboratories, Abbott Park, Ill.). Positiveanti-HEV results were noted with samples from three sites (Pakistan,U.S. and New Zealand), as explained hereinbelow.

One would expect to observe higher seroprevalence rates amongpopulations “at risk” for exposure to HGBV and among individuals withnon-A-E hepatitis, than among populations considered to be at “low risk”for exposure to HGBV.

The second objective of the serological studies was to examine specimensfound to be positive for antibodies to one or more HGBV epitopes byRT-PCR to determine if the virus is present in serum. It is well knownthat HBV and HCV can establish a viremic state which persists for monthsor years, and in general, that HAV and HEV establish a short-livedviremia persisting in general for several weeks. In cases of HBV and HCVinfection which are acute, resolving hepatitis, the viremic stage mayalso be short-lived persisting for several weeks. Thus, RT-PCR can beused to provide evidence that the virus is present in an infectedindividual. However, because the viremic state can be short-lived, anegative RT-PCR result for a given agent can be observed in individualswho are infected with that agent.

G. Cutoff Determination

Previous experience with other ELISA's utilizing the indirect assayformat indicated that a preliminary cutoff value can be calculated basedon the absorbance values obtained on a population presumably negativefor antibodies to the protein being studied. A preliminary cutoff valuewas calculated as the sum of the mean absorbance value of the populationplus 10 standard deviations from the population mean. Since the cutoffvalue was to be used every time a panel was run, a more convenientmethod to express the cutoff was as a factor of the negative control(pool of normal human plasma—NHP) which was run in replicates of fivefor each assay run. For the 1.7, 1.4 and 4.1 ELISA's, the negativecontrol typically had an absorbance value of between 0.030 and 0.060. Asdescribed below, the cutoff values were calculated to be at anabsorbance value of approximately 0.300 to 0.600, which was equivalentto an absorbance signal of ten times the negative control value. Thus,in order for a specimen to be considered reactive, the ratio of thesample (S) absorbance value to the negative (N) control absorbance value(S/N ratio) had to be equal to or greater than 10.0.

H. Supplemental Testing

Specimens which were initially reactive were typically retested induplicate. If one or both of the retest absorbance values were above thecutoff value, the specimen was considered repeatably reactive. Specimenswhich were repeatably reactive were then tested with supplemental assayswhich may further support the ELISA data. Repeatably reactive specimenswhich had sufficient volume may be tested by Western blot to determinethat the antibody response was directed against the CKS-1.7 (SEQUENCEI.D. NO. 610), a CKS-1.4 (SEQUENCE I.D. NO. 611) or CKS 4.1 (SEQUENCEI.D. NO. 612) antigens and not to E. coli proteins which may have beenco-coated on the solid phase with the major protein of interest. For aWestern blot result to be considered positive, a visible band had to bedetected at 80kD for the 1.7 protein (SEQUENCE I.D. NO. 610), 60-70 kDfor the 1.4 protein (SEQUENCE I.D. NO. 611) or at 42 kD for the 4.1protein (SEQUENCE I.D. NO. 612). Since the Western blot has not beenoptimized to match or exceed the sensitivity of the ELISA's, a negativeresult was not used to discard the ELISA data. However, a positiveresult reinforced the reactivity detected by the ELISA's.

Repeatably reactive specimens which had sufficient volume may be testedby RT-PCR (performed as described in Example 15.D using clone 4 primersto identify HGBV specific nucleotide sequences in serum. A positiveresult would indicate a viremic specimen and would ultimately help inestablishing the role of HGBV in human hepatitis. A negative result,however, was not to be construed to indicate that the ELISA results wasincorrect. As noted in the tamarin study in Example 15.E, RT-PCR resultswere positive in the first several weeks after infection and then becamenegative at about the time when antibodies were just beginning to bedetected with the current ELISA's. These later specimens may be RT-PCRnegative but positive in one or both of the ELISA's.

I. Serological Data Obtained with Low-Risk Specimens

A population consisting of 100 sera and 100 plasma was obtained fromhealthy, volunteer blood donors in Southeastern Wisconsin and tested forantibodies to the 1.7 (SEQUENCE I.D. NO. 610) and 1.4 (SEQUENCE I.D. NO.611) and 4.1 (SEQUENCE I.D. NO. 612) recombinant proteins utilizing theELISA's described above. The absorbance values obtained with the 1.7,1.4 and 4.1 ELISA's for serum and plasma were plotted separately (FIGS.9-14).

For the 1.7 ELISA, the mean absorbance values for the serum and plasmaspecimens were 0.072 [with a standard deviation (SD) of 0.061] and 0.083(SD=0.055), respectively. Thus, for the 1.7 ELISA's, the tentativecutoff values for serum and plasma were 0.499 and 0.468, respectively.As discussed above, the cutoff also was expressed as a factor of thenegative control absorbance value: specimens having S/N values above10.0 were considered reactive. Using this cutoff value, 0 of 200specimens tested for antibodies to 1.7 (SEQUENCE I.D. NO. 610).

For the 1.4 ELISA, several specimens (three from the serum populationand six from the plasma population) had absorbance values greater than0.300 (S/N's of 6-12, near or above the expected cutoff value). Whenretested, all nine of these specimens produced S/N values of less than10.0. The mean absorbance value for the serum and plasma specimens were0.072 (SD=0.052) and 0.108 (SD=0.062), respectively. The cutoff for the1.4 ELISA was calculated using the formula described above; the cutoffvalues for serum and plasma populations were 0.436 and 0.542,respectively. One specimen from the serum population was initiallyreactive and when re-tested in duplicate was negative. Two specimensfrom the plasma population were initially reactive but were negativeupon re-test. A second population of 200 normals was tested including100 plasma and 100 serum. Using the proposed cutoff, two plasma and twosera were repeatably reactive.

For the 4.1 ELISA, the mean absorbance values for the serum and plasmaspecimens were 0.070 [with a standard deviation (SD) of 0.037] and 0.063(SD=0.040), respectively. Thus, for the 4.1 ELISA, the tentative cutoffvalues for serum and plasma were 0.329 and 0.511, respectively. Asdiscussed above, the cutoff also was expressed as a factor of thenegative control absorbance value; specimens having S/N values above10.0 were considered reactive. Using this cutoff value, 0 of 100 plasmaspecimens and 0 of 100 serum specimens were initially reactive forantibodies to 4.1 (SEQUENCE I.D. NO.612).

An additional 760 plasma donors from the Interstate Blood Bank (Ohio)were tested with the 1.7 and 1.4 ELISAs. A total of 9 specimens wererepeatably reactive. None of the specimens were reactive in both ELISAs.All 9 specimens were repeatably reactive with the 1.4 ELISA.

In total, 960 specimens from plasma or blood donors residing in the U.S.were tested for antibodies to the 1.7 and 1.4 proteins. A total of 13specimens were repeatably reactive by the 1.4 ELISA. None of thespecimens were repeataby reactive with the 1.7 ELISA.

In summary, these data indicate that, with the existing ELISA's, a totalof 13 of 960 specimens obtained from U.S. blood donors were reactive forantibodies in one or more of the ELISA's employing recombinant antigensfrom HGBV-B. These data suggest that HGBV may be endemic in the U.S.

These data are summarized in TABLE 16.

J. Specimens Considered “At Risk” for Hepatitis

The data for these studies is summarized in TABLE 16.

(i) Specimens from West Africa

A total of 181 of 1300 specimens obtained from West Africa wererepeatably reactive in one or more of the ELISA's. One specimen wasrepeatably reactive in all 3 ELISA's. A total of 43 specimens wererepeatably reactive with the 1.7 ELISA, 91 specimens were repeatablyreactive with the 1.4 ELISA and 51 specimens were repeatably reactive inthe 4.1 ELISA.

One of six specimens repeatably reactive in the 1.7 ELISA was reactiveby Western blot for the 1.7 protein (SEQUENCE I.D. NO.610). Nine of 9specimens (100%) which were repeatably reactive in the 1.4 ELISA werepositive by Western blot for antibodies to the 1.4 protein (SEQUENCEI.D. NO. 611). One specimen was positive by Western blot for bothproteins. Twelve of 12 specimens (100%) repeatably reactive in the 4.1ELISA were positive by Western blot for the 4.1 protein (SEQUENCE I.D.NO.612.

Three repeatably reactive specimens (including one specimen positive inthe 1.4 ELISA and one specimen positive in both ELISA's and both Westernblots) were tested for HGBV RNA by RT-PCR using primers from clone 4 asdescribed above. All three specimens were negative by RT-PCR.

These data suggest that HGBV may be endemic in West Africa.

(ii) Specimens from Intravenous Drug Users (IVDU's)

Set 1: Three of 112 specimens were positive with the 1.4 ELISA. Fivespecimens were reactive on 4.1 ELISA and three on 1.7 ELISA. Two sampleswere positive on more than one ELISA.

Set 2: A total of 99 specimens were obtained from a population ofintravenous drug users, as part of a study being conducted at HinesVeteran's Administration Hospital, in Chicago, Ill. None of thesespecimens were reactive in the 1.7 or 4.1 ELISA. One specimen wasrepeatably reactive in the 1.4 ELISA. This repeatably reactive specimenwas tested for HGBV RNA by RT-PCR using primers from clone 4 asdescribed above. This specimen was RT-PCR negative.

K. Specimens Obtained from Individuals with Non A-E Hepatitis

The data for these studies is summarized in TABLE 16.

Various populations of specimens were obtained from individualsdiagnosed as having non-A-E hepatitis and tested with the 1.7, 1.4, and4.1 ELISA's described in Example 15.C. These specimens included: 180specimens obtained from a Japanese clinic; 56 specimens from a clinic inNew Zealand; 73 specimens obtained from a clinic in Greece; 132specimens from a clinic in Egypt; 64 specimens from a U.S. clinic inTexas (set T), 72 specimens from a research center in Minesota (set M);62 specimens from U.S. (set #1); 82 specimens obtained from a clinic inPakistan; 10 specimens from a clinic in Italy. (Due to insufficientvolumes of some sera, certain specimens from these groups were nottested on all of the available ELISAs).

(i) Specimens from Japan

These 180 specimens were obtained from 85 different patients. These tworeactive specimens came from 2 individuals. A total of 2 of 180specimens were repeatably reactive in the 1.7 ELISA. These 2 specimenswere tested by RT-PCR using primers from clone 4 as described above.None of the specimens were positive.

None of the specimens were positive in the 1.4 ELISA.

For the 4.1 ELISA, seven of 89 specimens were repeatably reactive in the4.1 assay. (Note: these 89 specimens were obtained from 29 differentpatients). Five of the reactive specimens were obtained from onepatient. The remaining two were from a different patient.

(ii) Specimens from New Zealand

A total four of 56 specimens were repeatably reactive in one or more ofthe ELISA's 1.7, 1.4, and 4.1. None of these specimens were reactive intwo or more ELISA's. One specimen was repeatably reactive in the 1.7ELISA and two specimens were repeatably reactive in the 1.4 ELISA. Onespecimen was repeatably reactive with the 4.1 ELISA. PCR was performedon two repeatably reactive specimens; both specimens were negative. Onespecimen which was repeatably reactive in the 1.4 ELISA was alsoreactive for antibodies to HEV.

(iii) Specimens from Greece

A total of 5 of 73 specimens were found to be reactive for antibodies inthe 1.7 and/or 1.4 ELISA's. These 73 specimens were obtained from atotal of 11 patients. Two of the five repeatably reactive specimens wererepeatably reactive for both ELISA's and were obtained from oneindividual on different dates. Two repeatably reactive specimens weretested by RT-PCR and were negative. None of these specimens werereactive for antibodies with the 4.1 ELISA.

(iv) Specimens from Egypt

A total of 11 of 132 specimens were reactive in the 1.7, 1.4, or 4.1ELISA's. Eight specimens were positive in both the 1.7 and 1.4 ELISA's.Nine specimens were reactive for antibodies in the 1.7 ELISA and 9specimens were reactive in the 1.4 ELISA. One specimen repeatablyreactive in the 4.1 ELISA but negative in the 1.7 and 1.4 ELISAs. Onespecimen repeatably reactive in the 1.7 ELISA was tested by Western blotand was negative for antibodies to the 1.7 recombinant protein (SEQUENCEI.D. NO. 610). Six of nine specimens repeatably reactive in the 1.4ELISA tested positive by Western blot for antibodies to the 1.4recombinant protein (SEQUENCE I.D. NO. 611). Seven of the repeatablyreactive specimens were tested by RT-PCR; none of the specimens werereactive. These 132 specimens were obtained on different dates from 25different individuals. The 11 repeatably reactive specimens wereobtained from five different individuals. For one of these individuals(patient #101), the immune response clearly mimics that observed withthe tamarins (FIG. 31). Note that in FIG. 31, the ALT levels wereelevated at the time of presentation of symptoms to the physician. Insubsequent specimens, the ALT levels declined and antibodies weredetected utilizing the 1.4 and 1.7 ELISA's. The antibody responsedeclined over the next several weeks as was noted with the serologicprofiles observed in the tamarins. Three additional patients (257, 260,and 340) exhibited serologic patterns similiar to patient #101 (as shownin FIGS. 32-34. These data provide supportive evidence that HGBV may bethe etiologic agent in these cases of hepatitis.

None of the seven specimens obtained from these four patients werepositive for HGBV RNA by RT-PCR. There are several potential reasons forthese results. First, the viremic phase may have been very short-lived:the virus may have been cleared from the serum by the time of the firstbleed date. Secondly, these specimens were shipped from Egypt and maypotentially have been frozen and thawed or otherwise compromised duringthe storage and shipping process, thus reducing the potential to detectHGBV RNA.

(v) Specimens from U.S. (Set T)

None of 64 specimens from the U.S. (set T) were repeatably reactive inthe 1.7, 1.4 or 4.1 ELISA.

(vi) Specimens from U.S. (Set M)

A total of 4 of 72 specimens from U.S. specimens (set M) were repeatablyreactive in one or more of the ELISA's. Two specimens were reactive withthe 1.7 and 4.1 ELISA's. One specimen was reactive only with 1.7 and onespecimen was reactive only with the 4.1 ELISA.

vii) Specimens from the United States (set 1)

A total of three of 51 specimens from non A-E hepatitis U.S. set 1 wererepeatably reactive in one or both of the ELISA's. One specimen wasrepeatably reactive in both ELISA's. One specimen was reactive in the1.7 ELISA and three specimens were repeatably reactive in the 1.4 ELISA.The specimen positive in both ELISA's was positive by Western blot forthe 1.4 recombinant protein (SEQUENCE I.D. NO. 22) but negative for the1.7 recombinant protein (SEQUENCE I.D. NO. 23). One additional specimenwas positive in the 1.4 ELISA and Western blot positive for the 1.4recombinant protein (SEQUENCE I.D. NO.611). One specimen which wasrepeatably reactive in the 1.4 ELISA was reactive for antibodies to HEV.

(viii) Specimens from Pakistan

A total of four of 82 specimens were repeatably reactive for antibodiesin 1.4 and/or 1.7 ELISAs. None of the specimens were reactive in bothELISA's. Two specimens were repeatably reactive in the 1.7 ELISA and twospecimens were repeatably reactive in the 1.4 ELISA. Two specimensrepeatably reactive in the 1.4 ELISA were also reactive for antibodiesto HEV. None of these 82 specimens were positive with the 4.1 ELISA.

(ix) Specimens from Italy

None of the ten specimens were repeatably reactive in the 1.7, 1.4, or4.1 ELISA.

L. Statistical Significance of Serological Results

These data indicate that specific antibodies to HGBV proteins (i.e.specimens repeatably reactive for antibodies in 1.7, 1.4, or 4.1 ELISA'scan be detected in all three categories of populations studied.Serological results obtained with the various categories of specimens(“low risk”, “at risk” and non A-E hepatitis patients) were groupedtogether and analyzed for statistical significance using the Chi squaretest. The data indicated that there is a significant difference incomparing the seroprevalence of anti-HGBV in volunteer blood donors witheither the individuals considered “at risk” for exposure to HGBV or toindividuals diagnosed with hepatitis of an unknown etiology.

Among West Africans, the seroprevalence rate is 13.9% and issignificantly higher than the baseline group (TABLE 17) with a p valueof 0.000. Similiarly, for the IVDU's, there was a statisticallysignificant difference (p value of 0.000) when the results from IVDU'swere compared with volunteer donors. In countries including Japan, NewZealand, U.S., Egypt, and Pakistan), there were significant differencesin antibody prevalence in patients with non A-E hepatitis when comparedto the volunteer blood donors from the US.

H. Summary

These data suggest that the ELISA's described herein may be useful indiagnosing cases of hepatitis in humans in various geographical regionsincluding Japan, New Zealand, U.S., Egypt, and Pakistan. It is likelythat these data underestimate the seroprevalence of antibodies to HGBVamong all categories of specimens tested. It is expected that asadditional HGBV epitopes are discovered and evaluated, the utility oftests derived from the HGBV genome(s) will become more important indiagnosing hepatitis among patients whose diagnosis cannot currently bemade. NOTE: Although the results of RT-PCR were negative in theseinitial studies, subsequent data revealed flavi-like vial sequences inserum of seropositive individuals (see Example 17).

As we have discussed supra, more than one strain of the HGBV is present.These are considered to be within the scope of the present invention andare termed “hepatitis GB Virus (“HGBV”).

Example 16 Serological Studies with HGBV-A

A. Recombinant Protein Purification Protocol

Bacterial cells expreessing the CKS fusion proteins were frozen andstored at −70 C. The bacterial cells from each of the GBV-A contstructswere thawed and disrupted as described in Example 15 for GBV-Bconstructs. Further, the recombinant proteins were purified as describedfor GBV-B recombinant proteins in example 15.

The fractions which were collected during the purification protocol wereelectrophoretically separated and stained with Coomassie Brilliant BlueR250 and examined for the presence of a protein having a molecularweight of approximately 60 kD (CKS 1.5/SEQUENCE NO. 614), 65 kD (CKS2.17/SEQUENCE NO. 613), 55 kD (CKS 1.18/SEQUENCE NO. 390) and 66 kD (CKS1.22/SEQUENCE NO. 390). Fractions containing the protein of interestwere pooled and re-examined by SDS-PAGE.

The immunogenicity and structural integrity of the pooled fractionscontaining the purified antigen were determined by immunoblot followingelectrotransfer to nitrocellulose as described in Example 13. In theabsence of a qualified positive control, the recombinant proteins wereidentified by their reactivity with a monoclonal antibody directedagainst the CKS portion of each fusion protein. When the CKS-1.5 protein(SEQUENCE I.D. NO. 614) was examined by Western blot, using the anti-CKSmonoclonal antibody to detect the recombinant antigen, a single band atapproximately 60 kD was observed. This corresponds to the expected sizeof the CKS-1.5 protein (SEQUENCE I.D. NO. 614). Similiarly, bands of theexpected sizes were noted for the CKS-2. 17 protein (SEQUENCE I.D. NO.613), the the CKS 1.18 protein (SEQUENCE NO. 390) and the CKS-1.22protein (SEQUENCE I.D. NO. 390) when examined by immunoblot.

B. Polystyrene Bead Coating Procedure

The proteins were dialyzed and evaluated for their antigenicity onpolystyrene beads described in Example 15.

C. ELISA Protocol for Detection of Antibodies to HGBV

The ELISA's were performed as described in Example 15.

D. Detection of HGBV RNA in Serum of Infected Individuals

Specimens which were repeatably reactive in the ELISAs were tested forHGBV RNA as described in section D. of Example 15.

E. Tamarin Serological Profiles

None of the sera from the tamarins produced a specific immune responsewhen tested in the ELISA utilizing the CKS 1.5 protein, the CKS 2.17protein, the CKS 1.18 protein or the CKS 1.22 protein, all derived fromthe HGBV-A genome. However, HGBV-A RNA was detected in several of theinfected tamarins as described in the previous example. (See Example 15for a summary of the tamarin serological profiles).

F. Experimental Protocol for Serologic Studies on Human Populations

In Example 15, ELISA's employing recombinant antigens from HGBV-B wereutilized to evaluate the presence of antibodies to HGBV-B in varioushuman populations. Many of the same specimens were then tested forantibodies to HGBV-A utilizing the 1.5 ELISA employing the CKS-1.5recombinant protein (SEQUENCE I.D. NO. 614), the 2.17 ELISA employingthe CKS-2.17 recombinant protein (SEQUENCE I.D. NO. 613), the 1.18 ELISAemploying the CKS-1.18 recombinant protein (SEQUENCE I.D. NO. 390), andthe ELISA employing the CKS-1.22 recombinant protein (SEQUENCE I.D. NO.390), coated on the solid phase (as described in Example 15). As notedin Example 15, all five of the convalescing tamarins inoculated withHGBV produced a specific but short-lived antibody response to the HGVB-Brecombinant proteins (as detected with the 1.7, 1.4 and 4.1 ELISA's).Although none of the tamarins produced a detectable antibody response inthe 1.5, 2.17, 1.18 or 1.22 ELISAs, some human specimens from WestAfrica produced a specific antibody response to one or more of theserecombinant proteins when tested via Western blot and one of thespecimens obtained from the surgeon (who was the source of the GB agent)at 22 days after onset of hepatitis produced a specific antibodyresponse to the 2.17 recombinant protein when tested by Western blot(see Example 3). In the current example, we evaluated the utility of the1.5, 2.17, 1.18 and 1.22 ELISA's in detecting antibodies in varioushuman populations.

G. Cutoff Determination

The cutoff for the 1.5, 2.17, 1.18, and 1.22 ELISAs were determined asdescribed in Example 15.

H. Supplemental Testing

As noted in Example 15, specimens which were initially reactive weretypically retested; if the specimen was repeatably reactive, additionaltests (e.g. Western blot) may be performed to further support the ELISAdata. For a Western blot result to be considered positive, a visibleband should be observed at 60 kD for the 1.5 protein (SEQUENCE I.D. NO.614) at 65 kD for the 2.17 protein (SEQUENCE I.D. NO. 613), at 55kD forthe 1.18 protein (SEQUENCE I.D. NO. 390) at 66 kD for the 1.22 protein(SEQUENCE I.D. NO. 390). Since the Western blot had not been optimizedto match or exceed the sensitivity of the ELISA's, a negative result wasnot used to discard the ELISA data. However, a positive resultreinforced the reactivity detected by the ELISA's.

As also noted in Example 15, repeatably reactive specimens which havesufficient volume may be tested by RT-PCR (performed as described inExample 15) using primers to identify HGBV specific nucleotide sequencesin serum.

I. Serological Data Obtained with Low-Risk Specimens

A total of 252 plasma specimens were obtained from the Interstate BloodBank in Ohio and tested for antibodies with the 1.5 ELISA which utilizesthe 1.5 recombinant protein (SEQUENCE I.D. NO. 614). The mean absorbancevalue for the population was 0.036 (SD=0.022). The cutoff was calculatedto be 0.168, corresponding to an S/N value of 10.0. A total of 760plasma specimens (including the 252 specimens utilized to determine thecutoff) were tested for antibodies with the 1.5 ELISA. None of thespecimens were repeatably reactive. In addition, 100 plasma specimenswere obtained from Southeastern Wisconsin and tested for antibodies withthe 1.5 ELISA. None of the specimens were repeatably reactive.

Thus, there is no evidence that antibodies to the 1.5 protein werepresent in U.S. blood donors.

A total of 200 specimens were obtained from Wisconsin blood donors andtested for antibodies with the 2.17 ELISA which utilizes the 2.17recombinant protein (SEQUENCE I.D. NO. 60). The mean absorbance valuefor the population was 0.058 (SD=0.025). The cutoff was calculated to be0.208, corresponding to an S/N value of approximately 10.0. One of thespecimens was repeatably reactive. Thus, the seroprevalence in U.S.blood donors (N=200) is relatively low.

The same 200 specimens described in the above paragraph were tested forantibodies with the 1.18 and 1.22 ELISAs. None of the specimens wererepeatably reactive. Thus, there is no evidence that specimens fromvolunteer blood donors are antibody positive for HGBV-A proteins asdetermine by the 1.5, 2.17, 1.18 and 1.22 ELISAs.

J. Specimens Considered “At Risk” for Hepatitis

The data for these studies is summarized in TABLE 18.

(i) Specimens from West Africa

A total of 58 of 1300 specimens were reactive with the 1.5 ELISA. Twelveof 18 repeatably reactive specimens were positive by Western blot forantibodies to the 1.5 protein (SEQUENCE I.D. NO. 614). A total of 43 of817 specimens were reactive in the 2.17 ELISA. These repeatably reactivespecimens were not tested by Western blot for antibodies to the 2.17protein (SEQUENCE I.D. NO. 613).

Six of the 817 specimens were reactive with the 1.22 ELISA. Nine of the353 specimens were reactive for 1.18 ELISA. Twenty-one specimensreactive with the 2.17 ELISA were tested by Western blot and 13 werereactive. All eight specimens that were repeatably reactive with the1.18 ELISA was positive by Western blot.

These data suggest that HGBV may be endemic in West Africa.

(ii) Specimens from Intravenous Drug Users

A total of 112 specimens were obtained from a population of intravenousdrug users, as part of a study being conducted at Hines Veteran'sAdministration Hospital, in Chicago, Ill. One specimen was repeatablyreactive in the 2.17 ELISA and an additional specimen was reactive inthe 1.18 ELISA. None of these specimens were positive in the 1.5 or 1.22ELISA.

K. Specimens Obtained from Individuals with Non A-E Hepatitis

The data for these studies is summarized in TABLE 18.

Various populations of specimens (described in Example 15.K) wereobtained from individuals with non-A-E hepatitis and tested with the1.5, 2.17, 1.18 and 1.22 ELISAs (described in Example 15.C). Due toinsufficient sample volume, not all specimens were tested in all of theELISAs.

(i) Specimens from Japan

A total of four of 89 specimens were repeatably reactive in the 1.5ELISA, with three of the specimens being from one individual and one ofthe specimens from a second individual. One specimen which had testednegative for the 1.5 ELISA, the 1.18 ELISA and the 1.22 ELISA wasreactive in the 2.17 ELISA. None of the specimens were reactive in the1.18 ELISA. These specimens were not tested with the 1.22 ELISA.

(ii) Specimens from New Zealand

None of these 56 specimens were reactive in the 1.5 ELISA. Thesespecimens were not tested in the 2.17 ELISA, the 1.18 ELISA or the 1.22ELISA.

(iii) Specimens from Greece

None of the 67 specimens (obtained from a total of 10 patients) werereactive for antibodies with the 1.5, 2.17 or 1.22 ELISA.

(iv) Specimens from Egypt

None of 132 specimens were reactive in the 1.5 ELISA. A total of 7 of132 specimens available for testing were reactive in the 2.17 ELISA.These specimens were obtained from 25 individuals with acute non A-Ehepatitis. Three of the 25 patients were seropositive in the 2.17 ELISAon one or more separate dates following the onset of hepatitis. Nonewere reactive in the 1.18 or 1.22 ELISA.

(v) Specimen from the U.S. (Set M)

None of the 72 specimens were reactive with the 1.5 ELISA. Three of the72 specimens were reactive for the 1.18 ELISA. Two of the specimens werereactive in the 2.17 ELISA and four specimens were reactive with the1.22 ELISA. Two of the samples were reactive in one of more of theELISAs.

(vi) Specimens from U.S. (Set T)

None of the 64 specimens were reactive with the 1.5, 1.22 or 2.17ELISAs. One specimen was reactive for the 1.18 ELISA.

(vii) Specimens from U.S. (Set 1)

A total of 3 of 62 specimens were reactive in one or more of the GBV-AELISAs. One specimen was repeatly reactive in both the 2.17 and 1.22ELISA. One specimen was reactive only in the 2.17 ELISA and anadditional specimen was reactive only in the 1.22 ELISA. None of thespecimens were reactive in the 1.5 or 1.18 ELISA.

As we have discussed supra, it is possible that more than one strain ofthe HGBV may be present, or that more than one distinct virus may berepresented by the sequences disclosed herein. These are considered tobe within the scope of the present invention and are termed “hepatitisGB Virus (“HGBV”).

L. Statistical Significance of Serological Results

These data indicated that specific antibodies to HGBV-A proteins (i.e.specimens repeatably reactive for antibodies in 1.5, 2.17, 1,18 and 1.22ELISA's) were detected among individuals considered “at risk” forexposure to HGBV and among individuals diagnosed with non A-E hepatitis,but were not frequently detected either among volunteer or paid blooddonors from the U.S. In TABLE 19, the serological results obtained withthe various categories of specimens (“low risk”, “at risk” and non A-Ehepatitis patients as shown in TABLE 18) were grouped together andanalyzed for statistical significance using the Chi square test. Unlikethe data in TABLE 18, which compiled the seroprevalence of antibodies toHGBV proteins in the total number of specimens tested, the data in TABLE19 reflect the results obtained with different individuals (persons).For the GBV-A ELISAs, the data indicate that there is a significantdifference (with a p value of 0.000) in comparing the seroprevalence ofanti-HGBV in volunteer blood donors with the individuals considered “atrisk” for exposure to HGBV (West Africa) but not in the IVDUs. Inaddition, there was a statistically significant difference between theseroprevalence of antibodies to HGBV-A in individuals with non A-Ehepatitis in Egypt and the U.S. when compared to volunteer donors Thesedata suggest that exposure to HGBV-A was associated with non-A through Ehepatitis. NOTE: although the results of RT-PCR were negative in theseinitial studies, subsequent data revealed flavi-like vial sequences inserum of seropositive individuals (see Example 19).

M Summary

These data suggest that the ELISA described herein may be useful indetecting antibodies among individuals residing in West Africa and amongindividuals with non-A through E hepatitis. The risk for hepatitis amongthe West Africans is relatively high; nearly 85% of these individualsare seropositive for antibodies to Hepatitis B virus, and approximately5% are positive for antibodies to hepatitis C virus. It is likely thatthese data underestimate the seroprevalence of antibodies to HGBV amongall categories of specimens tested. It is expected that as additionalHGBV epitopes are discovered and evaluated, the utility of tests derivedfrom the HGBV genome(s) will become more important in diagnosinghepatitis among patients whose diagnosis cannot currently be made.

Example 18

Identification of a GB-related Virus in Humans

A. Theory

Epitopes from both HGBV-A and HGBV-B have been identified (Example 3).These have been used as serologic markers to screen human serum andplasma samples (Examples 5 and 6). A significant correlation betweenseroreactivity with some of these markers and the incidence of nonA-Ehepatitis has suggested that HGBV-B is the causative agent of nonA-Ehepatitis in humans (Example 5.G). However, Western blot analysis of GBhuman sera gave no indication of reactivity to HGBV-B epitopes (Example3). Instead, at least one HGBV-A epitope was identified with the GBhuman sera suggesting that HGBV-A was the causitive agent of hepatitisin GB. Neither HGBV-A nor HGBV-B sequences have been identified inpatients with nonA-E hepatitis by RT-PCR (Example 5.E). Therefore, proofof HGBV-A and/or HGBV-B infection in humans with nonA-E hepatitisremains to be determined.

The failure to identify HGBV-A and/or HGBV-B sequences in human sera orplasma sources may be due to several factors. First, we have looked atonly a limited number of HGBV-A and/or HGBV-B-seropositive samples byRT-PCR, and the complete storage history of many of these samples isunknown. Thus, it is possible that viral RNA present in these sampleswas compromised by incorrect storage. Second, GB infection appears to beresolving in nature. As such, the window of time in which GB sequencesare present in an infected individual's serum may be very narrow. Thus,the chances of obtaining serum samples containing GB sequences may beextremely low. Finally, a limited number of PCR primer sets were used tolook for HGBV-A and/or HGBV-B sequences. HGBV-A and/or HGBV-B are RNAviruses and, therefore, are likely to have high rates of mutation(Holland, et al. (1982) Science 215:1577-1585). Thus, the sequence ofHGBV-A and/or HGBV-B present in the examined human sera may be differentenough from the sequence of our PCR primers such that HGBV-A and/orHGBV-B may be not be detected.

To address the possibility that the genomic variability of HGBV-A and/orHGBV-B prevented these viruses in our PCR studies, degenerate PCRprimers were designed to the highly conserved NS3-like regions of HGBV-Aand HGBV-B (see FIG. 17). It was reasoned that these highly conservedregions serve a necessary function in the viral replicative cycle.Therefore, these sequences should be maintained HGBV-A and HGBV-Bvariants. PCR primers designed within this region should be able todetect HGBV-A and/or HGBV-B genomic RNA by RT-PCR. In addition, bydesigning degenerate PCR primers that can specifically amplify HGBV-A,HGBV-B and HCV sequences, we reasoned that we might be able to amplifysequences from viruses related to HGBV-A, HGBV-B and HCV. Thus, if thelimited seroreactivity detected in human serum and plasma samples(Examples 5 and 6) is the result of cross-reactive antibodies toantigens from distinct HGBV-A- or HGBV-B-related viruses, we may be ableto obtain sequences from these GB-related viruses. [This is similar tothe experimental approach that Nichol and colleagues took to identifythe unique Hantavirus associated with the recent outbreak of acuterespiratory illness in the Southwest United States. Nichol, et al.Science 262:914-917 (1993)]

B. Cloning the NS3-like Region of Hepatitis GB Virus C (HGBV-C)

In several models of virus infetions, viremia occurs during the earlystages of infection and is often associated with the detection of IgMclass antibodies to viral proteins. As noted in examples 5 and 6,several specimens were immunoreactive in ELISA's which detected IgGclass antibodies to recombinant proteins derived from HGBV-A and HGBV-B.Additional ELISA's were performed to determine if IgM class antibodiescould be detected to these proteins. Several seropositive specimensobtained from West African individuals (Example 5.E.i) were reactive forIgM class antibodies to the recombinant proteins (data not shown). Thesespecimens were thought to have a high probability of containing virus.In addition, specimens obtained from HGBV-A- and HGBV-B-seropositiveEgyptian individuals (Example 5.F.vii) suffering from acute hepatitis inthe absence of detectable IgM class antibodies to HGBV-A or HGBV-Brecombinant proteins were also examined due to the likelihood that acuteliver disease is most likely linked to viral presence. A “hemi-nested”RT-PCR was performed on the nucleic acids from these samples withdegenerate oligonucleotide primers which will amplify HGBV-A, HGBV-B andHCV-1 sequences using the GeneAmp® RNA PCR kit (Perkin Elmer) asdirected by the manufacturer. Briefly, the first set of amplificationswere performed on the cDNA products of random-primed reversetranscription reactions of the extracted nucleic acids with 2 mM MgCl₂and 1 μM primers ns3.1-s and ns3.1-a (SEQUENCE ID. NOS. 671 and 672,respectively). Reactions were subjected to 40 cycles ofdenaturation-annealing-extension [three cycles of (94° C., 30 sec; 37°C., 30 sec; 2 min ramp to 72° C.; 72° C., 30 sec) followed by 37 cyclesof (94° C., 30 sec; 55° C., 30 sec; 72° C., 30 sec)] followed by a 10min extension at 72° C. Completed reactions were held at 4° C. Thesecond set of amplifications were as described above except that 4% ofthe first PCR products were used as the template, and ns3.1-s and ns3-a(SEQUENCE ID. NOS. 671 and 673, respectively) were used as the“hemi-nested” primer set. Products from the first and second sets ofPCRs were analyzed by gel electrophoresis.

One sample from West Africa had a PCR product from the hemi-nestedreaction that migrated at approximately 386 bp (the expected size of aHGBV-A, HGBV-B or HCV product). This product was cloned into pT7 BlueT-vector plasmid (Novagen) as described in the art. The sequenceobtained from this clone (GB contig C [GB-C], SEQUENCE ID. NO. 673,residues 2274-2640) was compared with GB contig A (GB-A, SEQUENCE ID.NO. 163, residues 4438-4804), GB contig B (GB-B, SEQUENCE ID. NO. 393,residues 4218-4587) and HCV-1 (SEQUENCE ID. NO. 398). FIG. 36 shows anucleotide alignment of these sequences, while TABLE 20 shows thepercent identity between these sequences.

TABLE 20 GB-A GB-B GB-C HCV-1 GB-A 100.0 47.99 61.66 52.55 GB-B 100.052.55 54.96 GB-C 100.0 57.37 HCV-1 100.0

As demonstrated in FIG. 36 and TABLE 20, nucleotide comparisons of GB-A,GB-B and HCV-1 show that these sequences are 47.99 to 61.66% identicalto one another. This is not surprising when one considers the conservedamino acid residues present in the NTP-binding helicase of these viruses(Example 2.B.3, FIG. 17A). The nucleotide comparison of the NS3 PCRproduct obtained from the West African sample (GB-C, SEQUENCE ID. NO.673, residues 2274-2640) with the other viruses suggests that the WestAfrican NS3 product (GB-C, SEQUENCE ID. NO. 673, residues 2274-2640) isrelated to, but distinct from the NS3 sequences from GB-A (SEQUENCE ID.NO. 163, residues 4438-4804), GB-B (SEQUENCE. ID. NO. 393, residues4218-4587) and HCV-1 (SEQUENCE ID. NO. 398). This sequence comparisonsuggests that GB-C may be from a GB-like virus more closely related toGB-A than GB-B or HCV. BLASTN and BLASTX searches of nucleic acid andprotein databases in the Wisconsin Sequence Analysis Package (Version 8)with GB-C (SEQUENCE ID. NO. 673, residues 2274-2640) finds limitedsequence identity with several strains of HCV. The highest P values(i.e., adds of alignment being made by chance) for nucleotide and aminoacid searches were 1.9×10⁻²⁰ and 5.3×10⁻³¹, respectively (data notshown). Together, these data suggest that GB-C (SEQUENCE ID. NO. 673,residues 2274-2640) may be from a unique GB-like virus related toHGBV-A, HGBV-B and HCV which we now designate, HGBV-C.

C. GB-C is Exogenous

PCR primers to GB-C sequence were utilized to determine whether thissequence could be detected in the genomes of humans, Rhesus monkeys, S.cerevisiae and E. coli as described, for example, in Example 6.B. PCRwas performed using GeneAmp® reagents from Perkin-Elmer-Cetusessentially as directed by the supplier's instructions. Briefly, 300 ngof genomic DNA was used for each 100 μl reaction. PCR primers (SEQUENCEI.D. NOS. 675 and 676) were used at a final concentration of 1.0 μM. PCRwas performed for 40 cycles (94° C., 30 sec; 55° C., 30 sec; 72° C., 30sec) followed by an extension at 72° C. for 10 min. PCR products wereseparated by-agarose gel electrophoresis and visualized by UVirradiation after direct staining of the nucleic acid with ethidiumbromide, followed by hybridization to a radiolabeled probe afterSouthern transfer to a Hybond-N+ nylon filter. FIG. 37 shows aPhosphoImage (Molecular Dynamics, Sunnyvale, Calif.) from a Southernblot of the PCR products after hybridization with the radiolabeled probefrom GB-C (SEQUENCE I.D. NO. 673, residues 2274-2640). GB-C (SEQUENCEI.D. NO. 673) sequences were not detected in human (FIG. 19, lane 1),Rhesus monkey (lane 2), S. cerevisiae (lane 3) or E. coli (lane 4)genomic DNAs despite the detection of ˜350 fg (one genome copyequivalent, lane 5) and ˜35 fg (0.1 genome copy equivalents, lane 6) ofGB-C plasmid template in 300 ng human genomic DNA. (Lane 7 contains thePCR products from ˜3.5 fg [0.01 genome copy equivalents] GB-C plasmidtemplate in 300 ng human genomic DNA.) Thus, using genomic PCR that candetect 0.1 genome copy equivalents, GB-C (SEQUENCE I.D. NO. 673) cannotbe detected in the genomes of human, Rhesus monkey, S. cerevisiae, andE. coli. These data are consistent with the purported exogenous (i.e.viral) origin of GB-C (SEQUENCE I.D. NO. 673).

D. GB-C can be Detected in Additional Human Serum Samples

Additional HGBV-A and HGBV-B immunoreactive human serum samples weretested for the presence of GB-C sequences using RT-PCR. As in Example 7,nucleic acids extracted from serum samples were reverse transcribedusing random hexamers, and cDNAs were subjected to 35-40 cycles ofamplification (94° C., 30 sec; 55° C., 30 sec; 72° C., 30-90 sec)followed by an extension at 72° C. for 10 min. GB-C-specific PCR primers(g131-s1 and g131-a1, SEQUENCE ID. NOS. 675 AND 676) were used at 1.0 μMconcentration. The PCR products were separated by agarose gelelectrophoresis and visualized by UV irradiation after direct stainingof the nucleic acid with ethidium bromide and hybridization to aradiolabeled probe after Southern transfer to a Hybond-N+ nylon filter.A total of 48 HGBV-immunopositive samples were tested from West Africa.Including the original sample from which GB-C was identified, eightsamples from West Africa were positive for GB-C sequences by RT-PCR. Atotal of ten GB seronegative West African serum samples were tested,none of which had detectable GB-C sequences. PCR products from four ofthe positive samples were cloned and sequenced as described above. Overthe 156 nucleotides examined, two of four clones examined were identicalto GB-C sequence (SEQUENCE I.D. NO. 673, residues 2274-2640), and twoclones (SEQUENCE I.D. NOS. 677 and 678) contained sequences that were88.4% and 83.6% identical to GB-C (SEQUENCE I.D. NO. 673, residues2274-2640) (FIG. 38). However, despite the divergence at the nucleotidelevel, the predicted translation product of each clone is remarkablysimilar with only one amino acid change occurring in the predictedtranslation of SEQUENCE ID NO. 678.

Additional serum samples from individuals with nonA-E hepatitis fromGreece, Egypt and the United States were tested for GB-C sequences asdescribed above. None of these samples contained detectable GB-Csequences. The lack of detection of GB-C sequences in these samples maybe due to several reasons (see above, Theory). However, the sequencevariation noted above between GB-C (SEQUENCE I.D. NO. 673, residues2274-2640) and the two GB-C variants (SEQUENCE I.D. NOS. 678 and 677)suggest that if the closely related HGBV-C's from West Africa can differby 15.1% at the nucleotide level, it is likely that the GB-C-specificPCR primers (g131-s1, g131-a1, SEQUENCE ID. NOS. 675 and 676) may nothybridize sufficiently to geographically distinct isolates of GB-C virusto generate a detectable PCR product. In this case, PCR primers designedto a more conserved region (5′ UTR) of the genome may allow thedetection of GB-C sequences in non-West African serum samples.

E. Extension of the HGBV-C Sequences

The PCR walking technique described in Example 2.A hereinabove wasutilized to obtain additional GB-C sequences. Briefly, total nucleicacid were extracted from the West African human serum originally used toidentify GB-C (SEQUENCE I.D. NO. 673, residues 2274-2640). This nucleicacid was reverse transcribed as described supra. The resultant cDNAswere amplified in 50 μl PCR reactions (PCR 1) as described by Sorensenet al. except that 2 mM MgCl₂ was used. Reactions were subjected to 35cycles of denaturation-annealing-extension (94° C., 30 sec; 55° C., 30sec; 72° C., 90 sec) followed by a 10 min extension at 72° C.Biotinylated products were isolated using streptavidin-coatedparamagnetic beads (Promega) as described by Sorensen et al. Nested PCRs(PCR 2) were performed on the streptavidin-purified products asdescribed by Sorensen et al. for a total of 35 cycles ofdenaturation-annealing-extension as described above. The resultantproducts and the PCR primers used to generate them are listed in TABLE21.

TABLE 21 Reaction Primer set PCR 1 Primer set PCR 2 Size of PCR productC.1 SEQ ID #679/SEQ ID #135 SEQ ID #680/SEQ ID #126 1250 bp  C.2 SEQ ID#681/SEQ ID #694 SEQ ID #686/SEQ ID #126 220 bp C.3 SEQ ID #682/SEQ ID#694 SEQ ID #683/SEQ ID #126 250 bp C.4 SEQ ID #684/SEQ ID #695 SEQ ID#685/SEQ ID #126 800 bp C.5 comp. of SEQ ID #679/ SEQ ID #90/SEQ ID #126750 bp SEQ ID #695 C.6 SEQ ID #688/SEQ ID #672 SEQ ID #92/SEQ ID #1261150 bp  C.7 SEQ ID #690/SEQ ID #695 SEQ ID #94/SEQ ID #126 550 bp C.8SEQ ID #692/SEQ ID #695 SEQ ID #96/SEQ ID #126 250 bp C.9 653/SEQ ID#135 654/SEQ ID #126 625 bp C.10 655/SEQ ID #694 656/SEQ ID #126 350 bpC.11 657/SEQ ID #694 658/SEQ ID #126 550 bp C.12 659/SEQ ID #695 660/SEQID #126 450 bp C.13 661/665 662/SEQ ID #126 750 bp C.14 663/FP3 (SEQ ID#13) 664/SEQ ID #126 550 bp C.15 666/125 667/SEQ ID #126 600 bp

In addition, a 1.3 kb product (C.16) was generated with oligonucleotideprimers SEQ ID # 669 and SEQ ID # 670using PCR 1 conditions describedabove. This product, together with those described in TABLE 21 wereisolated from agarose gels and cloned into pT7 Blue T-vector plasmid(Novagen) as described in the art.

The cloned products were sequenced as described in Example 5. Thesequences were assembled using the GCG Package (version 7) of programs.A schematic of the assembled contig is presented in FIG. 39. GB-C is9034 bp in length, all of which has been sequenced and is presented inSEQUENCE I.D. NO. 400-606. These SEQUENCE I.D.'s corresond to the threeforward translation frames.

Example 19 CKS-based Expression and Detection of Immunogenic HGBV-CPolypeptides

The HGBV-C sequences obtained from the walking experiments described inExample 17 (TABLE 13) were cloned into the CKS expression vectorspJO200, pJO201, and pJO202 using the restriction enzymes listed in TABLE22 (10 units, NEB) as described in Example 13. Two additional PCRclones, designated C.3/2 and C.8/12, were also expressed (FIG. 39). PCRproduct C.3/2 was generated using primers SEQUENCE I.D. NO. 681 and thecomplement of SEQUENCE I.D No. 685 and PCR product C.8/12 was generatedusing primers (SEQUENCE I.D. NO. 693 and its complement) as described inExample 9. The PCR products were cloned into pT7Blue as describedpreviously, then liberated with the restriction enzymes listed in TABLE22 and cloned into pJO200, pJO201 and pJO202 as above.

Two human sera which had indicated the presence of antibodies to one ormore of the CKS/HGBV-A or CKS/HGBV-B fusion proteins by the 1.7, 4.1 or2.17 ELISAS (see Examples 15 and 16) were chosen for Western blotanalysis. One of these sera (240D) was from an individual with nonA-Ehepatitis (Egypt) and the other (G8-81) was from a West Africanindividual “at risk” for exposure to HGBV (see Example 15). TheCKS/HGBV-C fusion proteins were expressed and transferred tonitrocellulose sheets as described above. The blots were preblocked asdescribed and incubated overnight with one of the human serum samplediluted 1:100 in blocking buffer containing 10% E. coli lysate and6mg/ml XL1-Blue/CKS lysate. The blots were washed two times in TBS,reacted with HRPO-conjugated goat anti-human IgG and developed asindicated above. The results are shown in TABLE 22.

Several of the HGBV-C proteins showed reactivity with one or the otherof the two sera, and three (C.1, C.6 and C.7) were chosen for use inELISA assays (see Example 20). Thus, samples previously identified asreactive with HGBV-A and/or HGBV-B proteins additionally show reactivitywith HGBV-C proteins. The reactivity with multiple proteins from the 3HGBV viruses may be due to cross-reactivity resulting from sharedepitopes between the viruses. Alternatively, this may be a result ofinfection with multiple viruses, or to other unidentified factors.

TABLE 22 HGBV-C Samples Reactivity Reactivity PCR Restriction with humanwith human product^(a) digest^(b) G8-81 serum 240D serum GB-C KpnI,XbaI + − C.1 EcoRI, XbaI + − C.3/2 EcoRI, XbaI − − C.4 KpnI, XbaI − −C.9 KpnI, PstI ND − C.10 EcoRI, XbaI ND − C.5 KpnI, XbaI +/− − C.6 KpnI,PstI + − C.7 NdeI-fill, BamHI − + C.8/12 KpnI, XbaI + − ^(a)PCR productis as indicated in previous TABLES or Examples. ^(b)Restriction digestsused to liberate the PCR fragment from pT7Blue T-vector. ND = not done.

Example 20 Serological Studies with GBV-C

A. Recombinant Protein Purification Protocol

Bacterial cells expressing the CKS fusion proteins were frozen andstored at −70 C. The bacterial cells from each of the GBV-C constructswere thawed and disrupted as described in Example 15 for GBV-Bconstructs. Further, the recombinant proteins were purified as describedfor GBV-B recombinant proteins in example 15.

The fractions which were collected during the purification protocol wereelectrophoretically separated and stained with Coomassie Brilliant BlueR250 and examined for the presence of a protein having a molecularweight of approximately 75 kD (CKS C.1/SEQUENCE I.D. NO. 404), 71 kD(CKS C.6/SEQUENCE I.D. NO. 404), and 49 kD (CKS C.7/SEQUENCE I.D.NO.404). Proteins bands of the expected molecular weight were observedfor the CKS-C.6 and CKS-C.7 recombinant proteins. For the CKS-C.1protein, a band was observed which corresponded to a molecular weight of62 kD rather than at the expected molecular weight of 75 kD. It isunclear why there are differences between the expected and observedprotein band. Fractions containing the protein of interest were pooledand re-examined by SDS-PAGE.

The immunogenicity and structural integrity of the pooled fractionscontaining the purified antigen were determined by immunoblot followingelectrotransfer to nitrocellulose as described in Example 13. In theabsence of a qualified positive control, the recombinant proteins wereidentified by their reactivity with a monoclonal antibody directedagainst the CKS portion of each fusion protein. When the CKS-C.1 protein(SEQUENCE I.D. NO.404) was examined by Western blot, using the anti-CKSmonoclonal antibody to detect the recombinant antigen, a single band atapproximately 65 kD was observed. This differs from the expected size of75 kD for the CKS-C.1 protein (SEQUENCE I.D. NO.404). Bands of theexpected sizes were noted for the CKS-C.6 protein (SEQUENCE I.D. NO.404), and the CKS C.7 protein (SEQUENCE I.D. NO. 404) were observed whenexamined by immunoblot.

B. Polystyrene Bead Coating Procedure

The proteins were dialyzed and evaluaed for their antigenicity onpolystyrene beads described in Example 15.

C. ELISA Protocol for Detection of Antibodies to HGBV

The ELISA's were performed as described in the previous Example 15.

D. Detection of HGBV RNA in Serum of Infected Individuals

Specimens which were repeatably reactive in the ELISAs were tested forHGBV RNA as described in section D. of the previous example 15.

E. Tamarin Serological Profiles

None of the sera from the tamarins produced a specific immune responsewhen tested in the ELISA utilizing the CKS-C.1 protein, the CKS-C.6protein, or the CKS C.7 protein, all derived from the HGBV-C genome. SeeExample 15 for a description of the tamarin serological profiles.

F. Supplemental Testing

As noted in Example 15, specimens which were initially reactive weretypically retested; if the specimen was repeatably reactive, additionaltests (e.g. Western blot) may be performed to further support the ELISAdata. For a Western blot result to be considered positive, a visibleband should be observed at 65 kD for the C.1 protein (SEQUENCE I.D. NO.404), at 71 kD for the C.6 protein (SEQUENCE I.D. NO. 404), or at 49 kDfor the C.7 protein (SEQUENCE I.D. NO. 404). Since the Western blot hadnot been optimized to match or exceed the sensitivity of the ELISA'S, anegative result was not used to discard the ELISA data. However, apositive result reinforced the reactivity detected by the ELISA's.

As also noted in Example 15, repeatably reactive specimens which havesufficient volume may be tested by RT-PCR (performed as described inExample 10 using primers corresponding to SEQUENCE I.D. NOS. 8 and 9) toidentify HGBV-C specific nucleotide sequences in serum.

G. Experimental Protocol

In example 15, ELISA's employing recombinant antigens from HGBV-B wereutilized to evaluate the presence of antibodies to HGBV-B AND HGBV-A invarious human populations. Many of the same specimens were then testedfor antibodies to HGBV-C utilizing the C.1 ELISA employing the CKS-C.1recombinant protein (SEQUENCE I.D. NO. 404), the C.6 ELISA employing theCKS-C.6 recombinant protein (SEQUENCE I.D. NO. 404), the C.7 ELISAemploying the CKS-C.7 recombinant protein (SEQUENCE I.D. NO. 404) coatedon the solid phase (as described in Example 14). As noted in Example 15,all five of the convalescing tamarins inoculated with HGBV produced aspecific but short-lived antibody response to the HGVB-B recombinantproteins (as detected with the 1.7, 1.4 and 4.1 ELISA's). Although noneof the tamarins produced a detectable antibody response in the C.1, C.6,C.7 ELISAS, some of the human specimens produced a specific antibodyresponse to the C.1, C.6, and C.7 recombinant protein when tested viaWestern blot (see Example 13) In the current example, we evaluated theutility of the C.1, C.6, and C.7 ELISA's in detecting antibodies invarious human populations.

H. Cutoff Determination

The cutoff for the C.1, C.6, and C.7 ELISAs were determined as describedin Example 15.

I. Serological Data Obtained with Low-Risk Specimens

A population consisting of 100 sera and 100 plasma was obtained fromhealthy, volunteer donors in Southeastern Wisconsin and tested forantibodies to three recombinant proteins from GBV-C including theCKS-C.1 (SEQUENCE I.D. NO. 404) protein in the C.1 ELISA, the CKS-C.6(SEQUENCE I.D. NO. 404) protein in the C.6 ELISA, and the CKS-C.7(SEQUENCE I.D. NO. 404) protein in the C.7 ELISA.

For the C.1 ELISA, the mean absorbance values for the serum and plasmaspecimens were 0.049 {with a standard deviation (SD) of 0.040} and 0.038(SD=0.029), respectively The cutoff for serum and plasma were calculatedto be 0.214 and 0.286, respectively. As discussed above, the cutoffvalue was also expressed as a factor of the negative control absorbancevalue; specimens having S/N values above 10.0 were considered reactive.Using this cutoff, 0 of 100 plasma specimens and 1 of 100 serumspecimens were initially reactive and repeatably reactive for antibodiesto the C.1 protein (SEQUENCE I.D. NO. 404).

For the C.6 ELISA, the mean absorbance values for the serum and plasmaspecimens were 0.102 { with a standard deviation (SD) of 0.046} and0.105 (SD=0.047), respectively. Cutoff values were set such thatspecimens having an S/N value of 10 or greater were considered reactiveUsing this cutoff, three specimens (two from the serum population andone from the plasma population) were repeatably reactive (having S/Nvalues of 10 or greater) for antibodies to the C.6 protein (SEQUENCEI.D. NO. 404).

For the C.7 ELISA, the mean absorbance values for the serum and plasmaspecimens were 0.061 {with a standard deviation (SD) of 0.040} and 0.050(SD=0.055), respectively. Cutoff values were set such that specimenshaving an S/N value of 10 or greater were considered reactive. Usingthis cutoff, none of the specimens were repeatably reactive forantibodies to the C.7 protein (SEQUENCE I.D. NO. 404).

Thus, there is evidence that antibodies to the C.1, C.6, or C.7 proteinsare present in approximately 1% of U.S. blood donors (N=200).

J. Specimens Considered “At Risk” for Hepatitis

The data for these studies is summarized in TABLE 23.

(i) Specimens from West Africa

A total of 20 of 137 specimens were reactive in one or more of theELISAs utilizing GBV-C proteins. A total of 12 of 97 were repeatablyreactive in the C.1 ELISA, 3 of 52 were repeatably reactive in the C.6ELISA, 5 of 137 specimens were reactive in the C.7 ELISA. Three of theC.1 reactive specimens were tested on Western blot and found to bereactive.

These data suggest that HGBV may be endemic in West Africa.

(ii) Specimens from Intravenous Drug Users

A total of 112 specimens were obtained from a population of intravenousdrug users, as part of a study being conducted at Hines Veteran'sAdministration Hospital, in Chicago, Ill. A total of 2 of 112 specimenswere repeatably reactive for one or more proteins. One specimen wasrepeatably reactive in the C.1 ELISA, one specimen was repeatablyreactive in the C.7 ELISA. None of these specimens were positive in theC.6 ELISA.

K. Specimens Obtained from Individuals with Non A-E Hepatitis

The data for these studies is summarized in TABLE 23.

Various populations of specimens (described in Example 15.K) wereobtained from individuals with non-A-E hepatitis and tested with the1.5, 2.17, 1.18 and 1.22 ELISAs (described in Example 15.C). Due toinsufficient sample volume, not all specimens were tested in all of theELISAs.

(i) Specimens from Japan

None of a total of 89 specimens were repeatably reactive in the C.1ELISA. Due to lack of specimen volume, the specimens were not tested forantibodies in the C.6 or C.7 ELISAs.

(ii) Specimens from Greece

A total of 67 specimens were tested with the C.1 and C.7 ELISAs. None ofthe specimens were reactive.

(iii) Specimens from Egypt

A total of 18 specimens of 132 specimens were reactive in one or moreELISA. None of the specimens were reactive in the C.1 ELISA. A total of15 specimens were reactive in the C.6 ELISA and three were reactive inthe C.7 ELISA.

(iv) Specimens from U.S. (M Set)

A total of 6 specimens were reactive in one or more ELISA. Two specimenswere repeatably reactive in the C.1 ELISA. Four specimens wererepeatably reactive in the C.6 ELISA. None of the specimens werereactive in the C.7 ELISA.

(v) Specimens from U.S. (T Set)

None of the 64 specimens were reactive in either the C.1 or the C.6ELISAs. One specimen was repeatably reactive in the C.7 ELISA.

(vi) Specimens from Various U.S. Clinical Sites (Set 1)

In total, three of 62 specimens were reactive in one or more ELISA's.One specimen was repeatably reactive in both the C.1 and C.6 ELISA's.Two specimens were repeatably reactive in the C.7 ELISA.

As we have discussed supra, it is possible that more than one strain ofthe HGBV may be present, or that more than one distinct virus may berepresented by the sequences disclosed herein. These are considered tobe within the scope of the present invention and are termed “hepatitisGB Virus (“HGBV”).

L. Statistical Significance of Serological Results

These data indicated that specific antibodies to HGBV-C proteins (i.e.specimens repeatably reactive for antibodies in C.1, C.6 and C.7ELISA's) were detected among individuals considered “at risk” forexposure to HGBV and among individuals diagnosed with non A-E hepatitis,and at low rate among volunteer or paid blood donors from the U.S. InTABLE 24, the serological results obtained with the various categoriesof specimens (“low risk”, “at risk” and non A-E hepatitis patients asshown in TABLE 23) were grouped together and analyzed for statisticalsignificance using the Chi square test. Unlike the data in TABLE 23,which compiled the seroprevalence of antibodies to HGBV proteins in thetotal number of specimens tested, the data in TABLE 24 reflect theresults obtained with different individuals (persons). For the GBV-CELISAs, the data indicate that there is a significant difference (with ap value of 0.000) in comparing the seroprevalence of anti-HGBV involunteer blood donors with the individuals considered “at risk” forexposure to HGBV (West Africa) but not for the IVDUs. In addition, therewas a statistically significant difference between the seroprevalence ofantibodies to HGBV-C in individuals with non A-E hepatitis in Egypt andthe U.S. when compared to volunteer donors These data suggest thatexposure to HGBV-C was associated with non-A through E hepatitis. NOTE:although the results of RT-PCR were negative in these initial studies,subsequent data revealed flavi-like vial sequences in serum ofseropositive individuals (see Example 19).

Example 21 Presence of HGBV-C in Humans with Non-A-E Hepatitis

The generation of HGBV-C-specific ELISAs allowed the identification ofimmunopositive sera from patients with non-A-E hepatitis (Example forHGBV-C serology). These sera, together with several HGBV-A and/orHGBV-B-immunopositive sera from individuals with documented cases ofnon-A-E hepatitis (TABLE 25) were examined by RT-PCR for HGBV-Csequences. To increase the likelihood of detecting HGBV-C variants,RT-PCR was performed using degenerate NS3 oligonucleotide primers in afirst round of amplification followed by a second round of amplificationwith nested GB-C-specific primers. Briefly, the first roundamplification was performed on serum cDNA products generated asdescribed in Example 6, using 2 mM MgCl₂ and 1 μM primers ns3.2-s1 andns3.2-a1 (SEQ. ID. NOS. 711 and 712, respectively). Reactions weresubjected to 40 cycles of denaturation-annealing-extension [three cyclesof (94° C., 30 sec; 37° C., 30 sec; 2 min ramp to 72° C.; 72° C., 30sec) followed by 37 cycles of (94° C., 30 sec; 50° C., 30 sec; 72° C.,30 sec)] followed by a 10 min extension at 72° C. Completed reactionswere held at 4° C. A second round of amplification was performedutilizing 2 mM MgCl₂, 1 μM GB-C-specific primers (SEQUENCE I.D. NOS. 675and 676), and 4% of the first PCR products as template. The second roundof amplification employed a thermocycling protocol designed to amplifyspecific products with oligonucleotide primers that may contain basepair mismatches with the template to be amplified [Roux, Bio/Techniques16:812-814 (1994)]. Specifically, reactions were thermocycled 43 times(94° C., 20 sec; 55° C. decreasing 0.3° C./cycle, 30 sec; 72° C., 1 min)followed by 10 cycles (94° C., 20 sec; 40° C., 30 sec; 72° C., 1 min)with a final extension at 72° C. for 10 minutes. PCR products wereseparated by agarose gel electrophoresis, visualized by UV irradiationafter direct staining of the nucleic acid with ethidium bromide, thenhybridized to a radiolabeled probe for GB-C after Southern transfer toHybond-N+ nylon filter. PCR products were cloned and sequenced asdescribed in the art.

Using the above methodology, GB-C.4, GB-C.5, GB-C.6 and GB-C.7 wereobtained. These sequences are 82.1-86.6% identical to GB-C (SEQUENCEI.D. NO. 400,bases 4167-4365). FIG. 40 displays the sequence differencesof GB-C.4, GB-C.5, GB-C.6 and GB-C.7 aligned to the homologous region ofGB-C in the predicted codon triplicates. As demonstrated, a majority ofthe nucleotide differences do not result in amino acid changes fromGB-C. This overall sequence conservation at the amino acid levelsuggests that GB-C.4, GB-C.5, GB-C.6 and GB-C.7 were derived fromdifferent strains of the same virus, HGBV-C. In addition, the level ofsequence divergence at the nucleotide level demonstrates that these PCRproducts are not a result of contamination with any of the previouslyidentified GB-C sequences.

Three of these individuals (the sources of GB-C.4, GB-C.5 and GB-C.7)had no evidence of infection with hepatitis A, hepatitis B or hepatitisC viruses. The presence of GB-C sequences in these individuals withhepatitis of unknown etiology suggests that HGBV-C is one of thecausative agents of human hepatitis. Serial samples were available fortwo of the individuals (containing GB-C.4 and GB-C.5). To follow theHGBV-C sequence in these samples, clone specific RT-PCRs were developed.Briefly, nucleic acids extracted from serum were reverse transcribedusing random hexamers as in Example 7. The resultant cDNAs weresubjected to 40 cycles of amplification (94° C., 30 sec; 55° C., 30 sec;72° C., 30 sec) followed by an extension at 72° C. for 10 min. GB-C.4-or GB-C.5-specific PCR primers (GB-C.4-s1 and GB-C.4-a1, or GB-C.5-s1and GB-C.5-a1, respectively) were used at 1.0 μM concentration. PCRproducts were separated by agarose gel electrophoresis, visualized by UVirradiation after direct staining of the nucleic acid with ethidiumbromide, then hybridized to a radiolabeled probe after Southern transferto Hybond-N+ nylon filter.

GB-C.4 was found in sera from an Egyptian patient with acute non-A-Ehepatitis. This patient was seropositive for a HGBV-A protein (seeHGBV-A ELISA Example). RT-PCR of five serial samples from the Egyptianpatient demonstrated a viremia that persisted for at least 20 days afternormalization of the serum ALT values (TABLE 26). The presence of GB-Csequence after serum ALT normalization suggested that HGBV-C mayestablish chronic infections in some individuals. However, the absenceof additional samples from this patient prevents a conclusion as to thechronic nature of HGBV-C. Additional samples are being pursued toresolve this question.

GB-C.5 was obtained from a Canadian patient with hepatitis associatedaplastic anemia. Each sample from this patient was seropositive in theC.7 ELISA (Example 20). GB-C.5 was detected in the samples obtained fromthe Canadian patient during aplastic anemia (day 13 post-presentation)and at the time of death (day 14, FIG. 41) using GB-C.5-specific primers(GB-C.5-s1 and GB-C.5-a1). However, GB-C.5-specific PCR failed to detectGB-C.5 sequence at the time of presentation (day 0, acute hepatitis) andon day 3 (liver failure). Thus, it is unclear whether GB-C.5 was presentbelow the limit of detection in the first samples. If so, HGBV-C mayhave been the causative agent of this patient's aplastic anemia.However, because GB-C.5 was detected by RT-PCR only during aplasticcrisis, GB-C.5 may have been acquired from a blood product administeredto combat the anemia. In this case, HGBV-C's association with aplasticanemia would be similar to HCV's [Hibbs, et al. JAMA 267:2051-2054(1992)].

Due to the distant relation of HGBV-C and HCV, it was of interest todetermine whether current methods for detecting HCV infection wouldrecognize human samples containing HGBV-C. Routine detection ofindividuals exposed to or infected with HCV relies upon antibody testswhich utilize antigens derived from three or more regions of HCV-1.These tests allow detection of antibodies to all of the known genotypesof HCV in most individuals [Sakamoto, et al. J. Gen. Virol. 75:1761-1768(1994); Stuyver, et al. J. Gen. Virol. 74:1093-1102 (1993)]. Secondgeneration ELISAs for HCV were performed on the samples that containHGBV-C as described in Example 10 (TABLE 25). One of the 4 samples thatcontain HGBV-C was seropositive for HCV antigens. A limited number ofhuman sera which are seronegative for HCV have been shown to be positivefor HCV genomic RNA by a highly sensitive RT-PCR assay[Sugitani, 1992#65]. A similar RT-PCR assay (as described in Example 9) confirmed thepresence of an HCV viremia in the seropositive sample. However, none ofthe HCV seronegative samples were HCV viremic. Therefore, although 1 ofthe 4 individuals containing HGBV-C sequences have evidence of HCVinfection, the current assays for the presence of HCV did not accuratelypredict the presence of HGBV-C. The one HCV-positive patient appears tobe co-infected with HGBV-C. It is unclear whether the hepatitis noted inthis patient was due to HCV, HGBV-C or the presence of both viruses.That HGBV-C and HCV are found in the same patient may suggest thatcommon risk factors exist for acquiring these infections.

Using the PCR protocol described above, GB-C sequences (˜85% identicalto the previous GB-C isolates shown in FIG. 41, data not shown) wereidentified in “normal” units of blood from two volunteer U.S. donorobtained in 1994. These units tested negative for HBV, HCV, and hadnormal serum ALT values. However, these units tested positive in the 1.4ELISA. Finding HGBV-C in at least two units of “normal” blood out of˜1000 units immunoscreened suggests that this virus is currently in theU.S. blood supply. However, using ELISAs developed from HGBV proteinsand nucleotide probes from HGBV sequences, we demonstrate that theseunits of blood can be identified.

The large amount of sequence variation in the various GB-C sequences(FIG. 41) should be noted. Although highly sensitive, PCR based assaysfor viral nucleic acids are dependent on the sequence match betweenoligonucleotide primers and the viral template. Therefore, because thePCR primers utilized in this study were located in a region of theHGBV-C genome that is not well conserved in various isolates, not allHGBV-C viremic samples tested may have been detected by the RT-PCRassays employed here. Utilization of PCR primers from a highly conservedregion of the HGBV-C genome, as have been found in the HCV 5′untranslated region [Cha, et al. J. Clin. Microbiol. 29:2528-2534(1991)], should allow more accurate detection of HGBV-C viremic samples.

TABLE 25 GB-C containing sera GB HCV HCV Sequence Origin Clinicalreactivity¹ ELISA² RNA GB-C.4 Egyptian Acute A 0.25 0 Hepatitis GB-C.5Canada HA-AA³ C 0.15 0 GB-C.6 U.S. history of C 11.51 + hepatitis GB-C.7U.S. hepatitis A 0.26 0 ¹Immunoreactivity detected to recombinant HGBVprotein(s) from virus A, B or C. ²Sample to cutoff values reported.Values ≧1 (underlined) are considered positive. ³hepatitis associatedaplastic anemia

TABLE 27 Egyptian Serial Samples Days post- 2.17 ELISA GB-C.4presentation ALT (U/l)¹ Reactivity² RT-PCR  0 128  61.0 + 10 78 62.9 +20 49 69.4 + 30 33 39.1 + 40 30 55.9 + ¹Upper limit of normal: 45 U/l.²Sample to normal reported. Values ≧10 are considered positive.

Example 21 Sequence Comparisons and Phylogentic Analysis

Information about the degree of relatedness of viruses can be obtainedby performing comparisons, i.e. alignments, of nucleotide and predictedamino acid sequences. Performing alignments of the HGBV sequences withsequences of other viruses can provide a quantitative assessment of thedegree of similarity and identity between the sequences. Thisinformation can then be used to develop a rationale for the taxonomicclassification of the HGBV viruses. In general, the calculation ofsimilarity between two amino acid sequences is based upon the degree oflikeness exhibited between the side chains of an amino acid pair in analignment. The degree of likeness is based upon the physical-chemicalcharacteristics of the amino acid side chains, i.e. size, shape, charge,hydrogen-bonding capacity, and chemical reactivity, thus, similar aminoacids possess side chains that have similar physical-chemicalcharacteristics. For example, phenylalanine and tyrosine are amino acidscontaining aromatic side chains and are, therefore, regarded aschemically similar. A discussion of the chemistry of amino acids can befound in any basic biochemistry textbook, for example, Biochemistry,Third Edition, Lubert Stryer, Editor, W. H. Freeman and Company, NewYork, 1988. The calculation of identity between two aligned amino acidsequences is, in general, an arithmetic calculation which counts thenumber of identical pairs of amino acids in the alignment and dividesthis number by the length of the sequence(s) in the alignment. Analogousto the method used for amino acid sequence alignments, the determinationof the degree of identity between two aligned nucleotide sequences is anarithmetic calculation which counts the number of identical pairs ofnucleotide bases in the alignment and divides this number by the lengthof the sequence(s) in the alignment. The calculation of similaritybetween two aligned nucleotide sequences sometimes uses different valuesfor transitions and transversions between paired (i.e. matched)nucleotides at various positions in the alignment; however, themagnitude of the similarity and identity scores between pairs ofnucleotide sequences are usually very close, i.e. within one to twopercent.

As has been stated earlier, limited identity exists between amino acidsequences of the HGBV agents and hepatitis C genotypes. In order to moreaccurately determine the degree of relatedness between the HGBV agentsand HCV, amino acid sequence alignments were performed using thesequence of the entire large open reading frame (ORF) of HGBV-A, B, andC, and the amino acid sequence of the large ORF of severalrepresentative HCV isolates. In addition, the degree of relatednessbetween the HGBV agents and HCV at the nucleotide level was determinedusing the entire genomic nucleotide sequence of HGBV-A, B, and C, andthat of several representative HCV isolates. Alignment of the amino acidand nucleotide sequences was performed using the program GAP of theWisconsin Sequence Analysis Package (Version 8) which is available fromthe Genetics Computer Group, Inc., 575 Science Drive, Madison, Wis.,53711. The gap creation and gap extension penalties were 5.0 and 0.3,respectively, for nucleic acid sequence alignments, and 3.0 and 0.1,respectively, for amino acid sequence comparisons. The GAP program usesthe algorithm of Needleman and Wunsch (J. Mol. Biol. 48:443-453, 1970)to calculate the degree of similarity and identity, expressed aspercentages, between the two sequences being aligned.

The nucleotide and amino acid sequences of selected members of the majorhepatitis C virus (HCV) genotypes were obtained from GenBank and areshown below with their respective accession numbers:

TABLE 27 HCV Isolate Genotype designation GenBank Accession Number HCV-11a M62321 HCV-JK1 1b X61596 HCV-J6 2a D00944 HCV-J8 2b D10988 HCV-K3a 3aD28917 HCV-Tr 3b D26556

Results of pairwise comparisons of the predicted amino acid sequences ofthe large open reading frame (i.e. putative precursor polyprotein) andthe nucleotide sequences between each of the above HCV genotypes andeach of the HGBV isolates are shown in Tables 28 and 29, respectively.The genotype designation, which is based on the system of nomenclaturefor HCV isolates described by Simmonds P. et al (1994) Hepatology,19:1321-1324, of each of the HCV isolates are shown in the top row.

The data shown in TABLE 28 demonstrate that the lower limit of aminoacid sequence identity between the HCV genotypes is 69%. This value isvery close to that shown by Simmonds et al. [Simmonds, P. et al.Hepatology, 19:1321-1324, 1994] who reported that comparisons of thecoding region (i.e. large open reading frame) of eight complete HCVgenomes from two major groups showed amino acid sequence similarities of67.1% to 68.6%; however, these authors did not describe the method bywhich the similarities were calculated. This value (69%) is also veryclose to the value of 71-84% identity reported by Okomoto et al.,[Virology, 188:331-341, 1992] for comparisons of HCV-J8 with other majorHCV isolates; however, these investigators did not describe the methodby which the identities were calculated. Comparisons of the HGBVpolyprotein sequences with each of the HCV genotypes reveals that theHGBV-encoded polyprotein sequences exhibit no more than 33% identity toany of the HCV polyproteins (TABLE 28). A comparison of the nucleotidesequences (TABLE 29) demonstrates a maximum sequence identity of 44.2%between any HGBV virus and any HCV isolate, whereas, the minimumnucleotide sequence identity between HCV isolates is 64.9%. Therefore,since HGBV-A, B, and C possess nucleotide and predicted amino acidsequence identity with HCV that is well outside the range of identitiesestablished for the known HCV genotypes, the HGBV viruses cannot beconsidered genotypes of the hepatitis C viruses.

The relationship between the hepatitis C viruses and the hepatitis GBviruses can be examined by performing phylogenetic analysis on theiraligned nucleotide or deduced amino acid sequences (i.e. large openreading frames) or on a portion of these sequences. This approach hasbeen applied to the hepatitis C viruses and showed that the variabilityof HCV isolates delineated six equally divergent main groups ofsequences [Simmonds, P. et al., J. Gen. Virol. (1993) 74:2391-2399 andSimmonds, P. et al., J. Gen. Virol. (1994) 75:1053-1061]. This analysisresulted in the establishment of a system of nomenclature for thehepatitis C viruses [Simmonds, P. et al. Hepatology, 19:1321-1324, 1994]where the isolates are classified into genotypes based upon theevolutionary distance between sequences.

In order to determine the phylogenetic relationship between thehepatitis GB viruses and the hepatitis C viruses, alignments of aminoacid sequences within the putative helicase gene of NS3 and the putativeRNA-dependent RNA-polymerase (RdRp) of NS5B were performed. Alsoincluded in the alignments were related sequences from other viruses inthe Flaviviridae and viruses that have been shown to possessevolutionary relatedness within their helicase or polymerase genes tomembers of the Flaviviridae [Koonin, E. V. & Dolja, V. V. (1993) Crit.Rev. Biochem. Mol. Biol. 28, 375-430 and Koonin, E. V. (1991) J. Gen.Virol. 72, 2179-2206].

The amino acid sequence alignments were made using the program PILEUP ofthe Wisconsin Sequence Analysis Package (version 8). Phylogeneticdistances between pairs of aligned sequences were determined using thePROTDIST program of the PHYLIP package (version 3.5c, 1993) kindlyprovided by J. Felsenstein [Felsenstein, J. (1989) Cladistics5:164-166]. These computed distances were used for the construction ofphylogenetic trees using the program NEIGHBOR (neighbor-joiningsetting). The trees were plotted using the program DRAWTREE. The treesshown are not rooted. The viral sequences used and their correspondingGenBank accession numbers are shown in TABLES 31. The evolutionarydistance between each HCV genotype and each of the HGBV viruses foralignments made within the helicase, RdRp, or complete large openreading frame are presented below in TABLES 32, 33, and 34 respectively.The distances calculated between the HCV genotypes or the HGBV virusesand the other viruses listed in TABLE 30 are not shown. The phylogenetictrees produced for amino acids alignments of the viral helicases, RdRps,or complete large open reading frames sequences are shown in FIGS. 42,43 and 44, respectively.

Amino acid sequence alignments of the putative RdRps, encoded within theNS5B region, of HGBV-A, B and C with the RdRp of several HCV genotypes,two of the pestiviruses, several representative flaviviruses, andseveral positive-strand RNA plant viruses, show that they possessconserved sequence motifs associated with the RdRps of positive-strandRNA viruses (data not shown). Based on similar analyses, the HGBV-A andHGBV-B encoded helicases show significant identity with the helicases ofthese positive-strand RNA viruses (data not shown), with the exceptionof CARMV, TCV, and MNSV which presumably do not possess helicase genes[Guilley, H et al. (1985) Nucleic Acids Res. 13:6663-6677]. Theseresults were not unexpected in view of the association of the helicaseand RdRp genes of these viruses into Supergroups demonstrated byprevious phylogenetic analyses [Koonin, E. V. & Dolja, V. V. (1993)Crit. Rev. Biochem. Mol. Biol. 28, 375-430]. However, examination of thephylogenetic distances between the HGBV isolates and the HCV isolatesbased upon alignment of the helicase or RdRp sequences (TABLES 30 and31) demonstrates that there is considerable distance between the membersof these two groups. The distances calculated demonstrate the closerelationship among the HCV genotypes, where the maximum distance betweenany two genotypes is 0.3696 (RdRp distance). However, the distancescalculated from the RdRp alignment between HGBV-A, -B, or -C and anymember of the HCV group is 0.96042-1.46261. Similarly, the distancescalculated from the helicase alignments for any two HCV genotype rangesfrom 0.044555-0.19706, while distances between any member of the HCVgroup and HGBV-A, -B, or -C ranges from 0.69130-0.87120. In addition,alignment of the predicted amino acid sequence of the entire large openreading frames of the HCV genotype and the GB viruses demonstrates anarrow range of evolutionary distance for the HCV isolates(0.17918-0.39646) while the minimum distance between any GB virus andany HCV isolate is 1.68650. Thus, the hepatitis GB viruses exhibitevolutionary distances that are clearly outside the range demonstratedfor the hepatitis C virus genotypes.

The phylogentic analysis of the HGBV and HCV sequences is attempting toanswer the question, “How does the divergence of the HGBV sequences fromthe HCV sequences compare with the divergence among the HCV sequences?In particular, might it be that the HGBV sequences are no more divergedfrom HCV sequences than the HCV sequences are from one another?” Areasonable condition to be met, if the HGBV sequences were no morediverged from HCV sequences than HCV sequences are from one another,would be that the HGBV-A, HGBV-B, and/or HGBV-C sequences would be atleast as close to one of the HCV sequences as the most distantly relatedpair of HCV sequences (i.e., the minimum distance from any HGBV sequenceto any HCV sequence is less than or equal to the maximum observeddistance among HCV sequences). This condition is not met by the presentsequence data; in Table 31 (RdRp alignment), the minimum HCV-HGBVdistance is 2.83 times the maximum HCV-HCV distance; and in Table 32(helicase alignment), the minimum HCV-HGBV distance is 3.51 times themaximum HCV-HCV distance. Thus, the data do not support the idea thatthe HGBV sequences are members of a group whose diversity is delimitedby previously characterized members of the HCV group.

The distribution of these relative distances can be examined with a testbased on the bootstrap [Efron, B. (1982) “The jackknife, the bootstrap,and other resampling plans”, Society Industrial and Applied Mathematics:Philadelphia; Efron, B. and Gong, G. (1983) “A leisurely look at thebootstrap, the jackknife, and cross-validation.” Am. Stat. 37: 36-48].The results obtained from the bootstrap sampling are shown in Table 32;which shows the comparison of the HCV-HGBV divergence (minimum of allHCV-HGBV distances) to the HCV diversity (maximum of all HCV-HCVdistances) based on PAM distances as calculated using the PROTDISTprogram. In 1000 bootstrap resamplings of the columns in the sequencealignments, the greatest divergence among HCV sequences was never aslarge as the smallest of the divergences of the HGBV sequences from theHCV sequences (Table 32). Thus, in independent measurements based onalignments of coding regions from two separate genes, there was not asingle instance in which the data were consistent with the HGBVsequences falling within the genetic sequence diversity of HCVgenotypes. Leaning in the direction of a conservative estimate, there isless than one chance in 100,000 that the data for the HGBVs could bedrawn from the same pool of sequences as the HCV sequences.

TABLE 32 (a) Distances Determined from RdRp AlignmentAlignment Out ofbootstrap 1000 samples: Average min(HCV-HGBV distance)/ = 2.543645 +/−max(HCV-HCV distance)  0.367443 Minimum min(HCV-HGBV distance)/ =1.617575 max(HCV-HCV distance) (b) Distances Determined from HelicaseAlignment Out of bootstrap 1000 samples: Average min(HCV-HGBV distance)/= 3.346040 +/− max(HCV-HCV distance)  0.511875 Minimum min(HCV-HGBVdistance)/ = 2.092055 max(HCV-HCV distance)

Assuming that the HCV sequences utilized in this study arerepresentative of the most divergent of the HCV genotypes, these resultsindicate that HGBV-A, B and C are not genotypes of HCV. In addition, itappears that HGBV-A and HGBV-C are more closely related to each otherthan either is to HGBV-B, which suggests that HGBV-A and HGBV-C may berepresentatives of a separate viral lineage. Similarly, HGBV-B may bethe sole representative of its own viral lineage. The relativeevolutionary distances between the viral sequences analyzed are readilyapparent upon inspection of the unrooted phylogentic trees presented inFIGS. 45 and 46, where the branch lengths are proportional to theevolutionary distance. The close evolutionary relationship of the HCVviruses is apparent and is consistent whether the analysis is performedusing a portion of the encoded genomic sequence or the entire genome(FIG. 44). The large degree of divergence between HGBV-A, HGBV-B, andHGBV-C and other Flaviviridae members demonstrate that, while being mostclosely related to the hepatitis C viruses, the GB-agents cannot beconsidered genotypes of HCV and may actually be representatives of a newvirus group, or groups, within the Flaviviridae.

The present invention thus provides reagents and methods for determiningthe presence of HGBV-A, HGBV-B and HGBV-C in a test sample. It iscontemplated and within the scope of the present invention that apolynucleotide or polypeptide (or fragment[s] thereof) specific forHGBV-A, HGBV-B and HGBV-C described herein, or antibodies produced fromthese polypeptides and polynucleotides, can be combined with commonlyused assay reagents and incorporated into current assay procedures forthe detection of antibody to these viruses. Alternatively, thepolynucleotides or polypeptides specific for the HGBV-A, HGBV-B andHGBV-C (or fragment[s] thereof) described herein, or antibodies producedfrom such polypeptides and polynucleotides (or fragment[s] thereof), canbe used separately for detection of the HGBV-A, HGBV-B and HGBV-Cviruses.

Other uses or variations of the present invention will be apparent tothose of ordinary skill of the art when considering this disclosure.Therefore, the present invention is intended to be limited only by theappended claims.

TABLE 2 T-1048 T-1053 T-1057 T-1061 ALT GGT ICD ALT GGT ICD ALT GGT ICDALT GGT ICD PRE-INOCULATION DAYS PRE 87 16 7 59 12 107 4 56 4 72 16 8 947 10 17 32 19 9 20 7 9 59 36 8 12 37 10 18 35 7 11 22 5 9 45 28 5 12 378 17 19 4 11 23 5 12 37 23 5 11 32 8 17 26 8 10 27 6 17 30 31 5 11 44 1018 18 7 10 24 6 14 24 25 5 10 39 9 18 34 3 12 24 7 10 17 19 4 11 49 1018 32 7 8 26 7 11  9 24 6 9 30 7 15 24 12 12 27 8 12  0 31 6 16 48 4 1721 9 8 19 2 15 POST INOCULATION DAYS POST  7 38 9 15 67 11 29 47 10 1332 8 12 11 172 15 53 14 63 39 Sactificed 198 34 90 48 7 16 21 93 28 57137 180 22 68 11 42 28 138 42 71 179 197 45 69 19 34 35 115 37 64 156112 26 70 21 8 42 116 42 76 139 177 54 87 23 61 49 81 56 34 40 59 16 5920 41 56 56 34 42 29 26 12 59 30 45 63 42 18 25 29 13 11 91 34 60 77 337 15 35 9 12 37 22 29 84 35 6 17 26 10 12 38 15 23 91 41 7 19 33 7 12 1711 14 97 28 7 20 20 8 10 15 10 9 GB Challenge 105  36 11 22 46 23 14 208 13 112  28 8 9 30 13 11 19 10 12 119  35 6 18 27 7 10 24 11 15 CO 48.110.7 18.7 65.1 15.5 20.7 50.3 25.2 15.5 33.7 12.1 21.9

TABLE 3 T-1047 T-1042 ALT GGT ICD ALT GGT ICD PRE INOCULATION DAYS PRE87 79 12 99 6 72 40 6 18 27 4 8 59 48 5 20 37 6 8 45 60 10 19 24 5 8 3740 7 11 30 47 8 26 39 4 10 24 25 2 11 17 54 12 27 33 5 12  9 44 5 11  043 12 18 33 5 12 POST INOCULATION DAYS POST  7 33 10 15 30 6 9 11 14 499 18 32 6 8 21 33 6 13 48 8 12 28 38 7 12 28 5 11 35 44 8 15 38 7 11 4238 8 14 31 9 11 49 52 8 16 28 7 9 56 41 9 15 21 6 11 CO 73.7 19.1 35.358.6 9.7 16.1

TABLE 4 T-1044 T-1034 ALT GGT ICD ALT GGT ICD PRE INOCULATION DAYS PRE87 102 6 97 72 19 5 11 42 6 12 59 23 6 11 12 11 12 45 37 6 12 32 6 10 3737 6 15 21 6 22 30 41 7 24 29 6 23 24 27 5 12 22 8 15 17 22 6 10 26 1012  9 31 4 12 30 4 11  0 40 4 14 19 3 17 POST INOCLUATION DAYS POST  734 6 14 27 8 13 11 14 39 8 16 28 12 13 21 36 6 10 21 8 16 28 37 6 9 14 913 35 35 5 10 19 9 12 42 27 4 9 32 8 13 49 59 7 13 33 7 14 56 24 4 12 309 12 63 30 5 11 31 9 12 67 21 7 9 39 11 10 CO 60.3 9.0 28.5 56.6 15.931.9

TABLE 5 T-1038 T-1049 T-1051 T-1055 ALT CGT ICD ALT CGT ICD ALT CGT ICDALT CGT ICD PRE INOCULATION DAYS PRE 115  82 9 102 13 41 15 97 34 100 42 4 15 23 9 9 31 6 13 30 3 9 87 30 8 13 28 7 12 41 6 11 73 45 5 16 6810 27 44 4 12 65 58 29 9 15 22 6 15 23 10 16 35 6 14 52 45 48 8 17 49 916 23 13 13 27 8 11 37 31 41 14 12 28 7 14 26 7 12 24 3 10 28 16 30 9 1429 9 13 15 5 8  0 32 16 10 24 6 15 27 9 11 23 7 10 POST INOCULATION DAYSPOST  7 30 12 10 42 5 15 27 6 18 150 11 21 11 81 18 42 79 15 33 66 13 42161 19 50 14 178 24 77 123 21 86 78 14 35 sacrificed sacrificedsacrificed 21 108 18 60 28 308 53 39 35 273 108 56 49 84 27 34 56 66 2834 63 72 28 29 69 41 18 19 76 28 11 13 83 44 12 15 90 43 7 16 CO 66.220.1 21.0 94.2 13.2 34.9 38.4 18.2 18.5 65.8 11.3 17.6

TABLE 8 HGBV CLONES Tamarin Plasma^(d) Genomic Pre-inoculation AcutePhase Clone size^(a) Southern^(b) PCR^(c) PCR RT-PCR PCR RT-PCR H205^(e)Northern^(f)  2 737 bp neg. ND 0/1 0/1 0/1 1/1 + ND  4 221 bp ND^(g)neg. ND 0/1 0/1 1/1 + ≧7 kb 10 307 bp ND neg. ND 0/1 0/1 1/1 + ND 16 532bp neg. neg. 0/1 0/7 0/1 4/6 + ND 18 306 bp ND neg. ND 0/1 0/1 1/1 + ND23 369 bp ND ND ND 0/1 ND 1/1 + ND 50 337 bp ND neg. ND 0/1 0/1 1/1 + ≧7kb ^(a)size of clone in base pairs (bp). ^(b)Southern blot analysis oftamarin, human, yeast and E. coli genomic DNA using GB clone sequence asa probe. Negative (neg.) indicates that the clone did not hybridize withany of the genomic DNAs tested. ^(c)Genomic PCR was performed ontamarin, human yeast and E. coli DNAs with primers that amplify thecloned sequence. Neg. indidcates that the clone was not amplified fromthe DNA sources tested. ^(d)Tamarin plasmas, both pre-HGBV-inoculation(pre-inoc.) and acute phase (acute) were tested for the presence ofcloned sequence by PCR (to detect DNA sequences) or RT-PCR (to detectRNA and DNA sequences). The results are reported as the number ofPCR-positive samples per number of samples examined. ^(e)H205 was testedfor the presence of the clones by RT-PCR. All clones were RT-PCRpositive (+) in H205 source. ^(f)Northern blot analysis was performed ontotal liver RNA from normal tamarin liver and acute phase tamarin liverusing radiolabel clone sequences. The estimated size of the specificband detected in the acute phase liver RNA is given. ^(g)ND: notdetermined.

TABLE 12 Days Pre (−) CORZYME HAVAB HCV 2.0 HEV or Post (+) A492 ResultA492 Result A492 S/N A492 S/N Sera Inoculation c/o = 0.582* c/o =0.662** c/o = 0.408*** c/o = >6**** Control Sera HuN/C 1.397 − 1.295 −0.070 − 0.038 − HuP/C 0.036 + 0.030 + 1.352 + 1.932 + Tamarin Sera T1048pre −44 N.D N.D N.D N.D N.D N.D 0.007 1.47 T1048 pre −23 0.912 − 1.834 −0.023 − N.D N.D T1048 post +112 1.148 − 1.387 − 0.025 − 0.026 0.68 T1051pre −52 N.D N.D N.D N.D N.D N.D 0.019 0.50 T1051 pre −8 0.548 + 1.465 −0.035 − N.D N.D T1051 post +76 0.700 − 1.559 − 0.043 − 0.029 0.76 T1057pre −30 N.D N.D N.D N.D N.D N.D 0.016 0.42 T1057 pre −23 0.369 + 1.411 −0.029 − N.D N.D T1057 post +49 N.D N.D N.D N.D N.D N.D 0.017 0.45 T1057post +77 0.580 + 1.444 − 0.028 − N.D N.D T1061 pre −30 N.D N.D N.D N.DN.D N.D 0.102 2.68 T1061 pre −23 0.248 + 0.029 + 0.040 − N.D N.D T1061post +112 0.240 + 0.048 + 0.030 − 0.077 2.03 *Cutoff was determined: 0.4× N/Cx + 0.6 × P/Cx **Cutoff was determined: N/Cx + P/Cx/2 ***Cutoff wasdetermined: N/Cx + 25% P/C ****Cutoff was determined: S/N > 6

TABLE 14 HGBV-A Samples Reactivity Reactivity Reactivity ReactivityReactivity with Reactivity with with with with PCR Restriction T1048 +with G1-41 G1-14 G1-31 341C product^(a) digest^(b) T1051 sera GB serumserum serum serum serum 1.2 EcoRI, PstI − − − − − − 1.5 EcoRI, HindIII −− + − − − 1.8 KpnI, PstI − − − − − − 1.17 KpnI, PstI − − ND ND − − 1.18KpnI, PstI − − ND ND − − 1.19 KpnI, PstI − − ND ND + + 1.20 KpnI, PstI −− ND ND − + 1.21 Xbal, BamHI − − ND ND − − 1.22 KpnI, PstI − + ND ND − −1.23 KpnI, PstI − − ND ND − − 2.17 BamHI, SphI − + ND ND + + 2.18 KpnI,PstI − − ND ND − − 4.2 EcoRI, blunt − − ND ND − − ^(a)PCR product is asindicated in Table 9, Table 10, or Example 13. ^(b)Restriction digestsused to liberate the PCR fragment from pT7Blue T-vector or for directdegestion of 4.2 PCR product. ND = not done.

TABLE 16 SEROLOGIC RESULTS HGBV- B POS/TOTAL 1.4 4.1 1.7 CATEGORYSPECIMENS ELISA* ELISA* ELISA* TOTAL Individuals Volunteer Blood DonorsAssumed 1  0/200  0/200  0/200  0/200 “Low Risk” for 2  4/200  4/200HGBV Exposure Interstate Blood Bank  9/760 ND**  0/760  9/760Individuals Intravenous Assumed Drug Users “At Risk” for 1  3/112  5/112 3/112  9/112 HGBV Exposure 2  1/99  0/99  0/99  1/99 Western Africa91/1300 51/1300 43/1300 181/1300 Hemophiliacs  2/100 ND  1/100  2/100Individuals with Clinics in Japan  0/180  7/89  2/180  9/180 “Non A-EClinics in Greece  4/73  0/67  3/73  5/73 Hepatitis” Clinics in U.S.(SET M)  1/72  2/72  3/72  4/72 Clinics in U.S. (SET T)  0/64  0/64 0/64  0/64 Clinics in U.S.  0/62  2/62  2/62  3/62 Clinics in Egypt 9/132  1/132  9/132  11/132 Clinics in New Zealand  2/56  1/56  1/56 4/56 Clinics in Costa Rica  2/100 ND  1/100  2/100 Clinics in Pakistan 2/82 ND  2/82  4/82 Clinics in Italy  0/10  0/10  0/10  0/10 Clinics inU.S. SET 1  0/56 ND**  0/56  0/56 SET 2  0/20 ND**  0/20  0/20 SET 3 3/51 ND**  1/51  3/51

TABLE 17 HGBV-B Serological Results Repeatably Reactive Negative In 1.4,1.7 or 1.4, 1.7 or 4.1 ELISA 4.1 ELISA X²* SIG** Volunteer Blood 0 200 —— Donors IBB Ohio 9 751 — ???* Intravenous Drug Users 1 99 — NS* (US) 9103 ??? West Africa 181 1119 ???^(•) Clinics in Japan 4 81 — ???*Clinics in New Zealand 4 52 — ???* Clinics in Greece 1 10 — ???* Clinicsin Egypt 5 20 — ???* in U.S. Set 1 0 56 NS* Set 2 0 20 NS* Set 3 3 51??? Set M 4 68 ???? Set T 0 64 NS* Assumed Low Risk 0 200 — — Paid BloodDonors 9 751 ??? Assumed High Risk 191 1321 ^(•)?? Non A-E Hepatitis 21431 — NS* *Chi square value obtained by applying the Chi square test.**Determination of statistical signficance based upon the Chi squareanalysis. ^(†)Not statistically significant by the Chi square test.^(•)Statistically signficant by the Chi square test, with p < 0.050.

TABLE 18 SEROLOGIC RESULTS - TABLE A POS/TOTAL 1.18 2.17 1.22 1.5 TOTALCATEGORY SPECIMENS ELISA ELISA ELISA ELISA REACTIVE IndividualsVolunteer Blood Donors Assumed 1 0/200  1/200 0/200  0/200  1/200 “LowRisk” for 2 HGBV Exposure Interstate Blood Bank ND* ND ND  0/760  0/760Individuals Intravenous 1/112  1/112 0/112  0/112  2/112 Assumed DrugUsers “At Risk” for Western Africa 9/353 43/817 6/817 58/1300 91/1300HGBV Exposure Individuals with Clinics in Japan 0/89  1/89 ND  4/89 3/89 “Non A-E Clinics in Greece 0/67  0/67 0/67  0/67  0/67 Hepatitis”Clinics in (Mayo) 3/72  2/72 4/72  0/72  7/72 Clinics in U.S. (Thiele)0/64  0/64 0/64  0/64  1/64 Clinics in U.S. (1/3) 1/62  2/62 2/62  0/62 3/62 Clinics in Egypt 0/132  7/132 0/132  0/132  7/132 Clinics in NewZealand ND ND ND  0/56 ND *Separate ELISA's were developed and cutoffsdetermined **Not Done

TABLE 19 HGBV-A Serological Results Repeatably Reactive in Negative In1.18, 2.17, 1.18, 2.17, 1.22, or 1.5 1.22, or ELISA 1.5 ELISA X²* SIG**Volunteer Blood 1 199 — — Donors IBB Ohio 0 760 — NS* Intravenous DrugUsers (US) 2 110 NS* West Africa 91 1209 ???^(•) Clinics in Japan 2 83 —???* Clinics in New Zealand 0 56 — NS* Clinics in Greece 0 11 — NS*Clinics in Egypt 3 22 — ???* in U.S. Set 1 ND ND — Set 2 ND ND — Set 3ND ND — Set M 7 65 ??? Set T 1 63 ??? Assumed Low Risk 1 200 — — PaidBlood Donors 0 760 NS* Assumed High Risk 93 1319 ???^(•) Non A-EHepatitis 13 300 — ?????* *Chi square value obtained by applying the Chisquare test. **Determination of statistical signficance based upon theChi square analysis. ^(†)Not statistically significant by the Chi squaretest. ^(•)Statistically signficant by the Chi square test, with p <0.050.

TABLE 23 SEROLOGIC RESULTS HGBV-C POS/TOTAL CATEGORY SPECIMENS C.7ELISA* C.1 ELISA* C.6 ELISA* TOTAL Individuals Volunteer Blood DonorsAssumed 1 0/200  1/200  3/200  4/200 “Low Risk” for 2 HGBV ExposureInterstate Blood Bank ND** ND** ND** ND** Individuals Intravenous 1/112 1/112  0/112  2/112 Assumes Drug Users “At Risk” for Western Africa5/137 12/97  3/52 20/137 HGBV Exposure Individuals with Clinics in JapanND**  0/89 ND**  0/89 “Non A-E Clinics in Greece 0/67  0/67 ND**  0/67Hepatitis” Clinics in U.S. (SET M) 0/72  2/72  4/72  6/72 Clinics inU.S. (SET T) 1/64  0/64  0/64  1/64 Clinics in U.S. (SET 1/3) 2/62  1/62 1/62  3/62 Clinics in Egypt 3/132  0/132 15/132 18/132 Clinics in NewZealand ND** ND** ND** ND**

TABLE 24 HGBV-C Serological Results Repeatably Reactive Negative In inC.1, C.6, C.1, C.6, or C.7 or C.7 ELISA ELISA X²* SIG** Volunteer Blood4 196 — — Donors IBB Ohio ND ND — NS* Intravenous Drug Users (US) 2 110NS* West Africa 20 117 ???? Clinics in Japan 0 85 — NS* Clinics in NewZealand ND ND — NS* Clinics in Greece 0 11 — NS* Clinics in Egypt 6 19 —???? in U.S. Set 1/3 3 59 ???? Set M 6 66 ??? Set T 1 63 NS* Assumed LowRisk 0 200 — — Paid Blood Donors 9 751 ??? Assumed High Risk 191 1330???^(•) Non A-E Hepatitis 21 303 — ???* *Chi square value obtained byapplying the Chi square test. **Determination of statistical signficancebased upon the Chi square analysis. ^(†)Not statistically significant bythe Chi square test. ^(•)Statistically signficant by the Chi squaretest, with p < 0.050.

TABLE 28 Amino acid sequence similarity (identity) across large ORFs(%). genotype: 1a 1b 2a 2b 3a 3b isolate: HCV-1 JK1 J6 J8 K3A Tr HGBV-AHGBV-B HCV-JK1 91 (85) HCV-J6 84 (72) 83 (72) HCV-J8 84 (72) 83 (71) 92(84) HCV-K3A 85 (74) 84 (75) 91 (84) 82 (70) HCV-Tr 84 (74) 84 (73) 82(69) 81 (69) 91 (84) HGBV-A 49 (26) 52 (31) 49 (28) 50 (28) 48 (26) 47(27) HGBV-B 52 (32) 49 (27) 52 (33) 52 (33) 50 (31) 50 (31) 49 (27)HGVB-C 51 (29) 49 (27) 51 (28) 50 (28) 51 (29) 50 (28) 66 (48) 51 (28)

TABLE 29 Nucleotide sequence identity across entire genomes (%)genotype: 1a 1b 2a 2b 3a 3b isolate: HCV-1 JK1 J6 J8 K3A Tr HGBV-AHGBV-B HCV-JK1 78.8 HCV-J6 67.8 68.0 HCV-J8 67.3 67.2 77.0 HCV-K3A 68.669.1 65.9 65.2 HCV-Tr 68.3 68.4 65.1 64.9 77.5 HGBV-A 41.6 41.8 41.541.0 41.6 41.6 HGBV-B 43.8 43.4 44.2 43.3 43.5 43.1 42.6 HGBV-C 42.942.3 42.1 42.1 41.1 41.5 53.3 41.6

TABLE 30 GenBank Accession numbers Virus GenBank Accession Number HCV-1M62321 HCV-JK1 X61596 HCV-J6 D00944 HCV-J8 D10988 HCV-Tr D26556 Dengue 1M87512 Dengue 2 M29095 BVDV, Bovine viral diahhrea virus M31182 HCHV,Hog cholera virus J04358 WNV, West nile virus M12294 YFV, Yellow fevervirus X15062 JEV, Japanese encephalitis virus M18370 CARMV, Carnationmottle virus X02986 TCV, Turnip crinkle virus M22445 MNSV, Melonnecrotic spot virus D12536 PBMSV, Pea seed-borne mosaic virus D10930PPV, Plum pox virus X16415 TVMV, Tobacco vien mottling virus X04083 TEV,Tobacco etch virus M15239

TABLE 31 Evolutionary distances: RdRp sequences. HGBV-A HGBV-C HCV-J6HCV-J8 HCV-1 HCV-JK1 HCV-3A HGBV-C 0.54878 HCV-J6 1.14632 1.43972 HCV-J81.16398 1.43043 0.11550 HCV-1 1.25705 1.36554 0.26824 0.26864 HCV-JK11.23506 1.46261 0.29041 0.29207 0.11347 HCV-3A 1.26876 1.40316 0.348800.36960 0.30535 0.35182 HGBV-B 1.14880 1.31596 1.00961 0.96402 1.073791.04486 1.01997

TABLE 32 Evolutionary distances: helecase sequences. HGBV-A HGBV-C HCV1HCVJK1 HCVJ6 HCVJ8 HCV3A HGBV-C 0.42074 HCV-1 0.86162 0.71571 HCV-JK10.87120 0.71731 0.04455 HCV-J6 0.85757 0.73261 0.14090 0.14079 HCV-J80.83480 0.72594 0.14200 0.14779 0.07495 HCV-3A 0.86537 0.77858 0.187030.19706 0.16267 0.17985 HGBV-B 1.02224 0.92174 0.72260 0.71806 0.720500.69130 0.73171

TABLE 33 Evolutionary distances: complete large open reading frames.HGBV-A HGBV-C HCVJ6 HCVJ8 HCV1 HCVJK1 HCV3A HGBV-C 0.92796 HCV-J62.41182 2.14894 HCV-J8 2.41162 2.16319 0.17918 HCV-1 2.38813 2.116440.35897 0.36481 HCV-JK1 2.40833 2.12664 0.36577 0.37948 0.17411 HCV-3A2.44255 2.15842 0.38848 0.39646 0.32500 0.32271 HGBV-B 2.68767 2.470391.69983 1.68650 1.71216 1.71657 1.73779

SEQUENCE LISTING The patent contains a lengthy “Sequence Listing”section. A copy of the “Sequence Listing” is available in electronicform from the USPTO web site(http://seqdata.uspto.gov/sequence.html?DocID=06720166B2). An electroniccopy of the “Sequence Listing” will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

What is claimed is:
 1. A purified HGBV polynucleotide, isolated from apositive stranded HGBV RNA genome, wherein said genome encodes apolypeptide, wherein said polypeptide consists essentially of an aminoacid sequence, at least 48% identical to the polypeptide sequence SEQ IDNO:387.
 2. A synthetic or recombinant HGBV polynucleotide, wherein saidpolynucleotide encodes a polypeptide which consists essentially of anamino acid sequence, at least 48% identical to the polypeptide sequenceSEQ ID NO:387.
 3. An expression system comprising said polynucleotide ofclaim 1, operably linked to a control sequence compatible with a desiredhost cell.
 4. A host cell transformed with said expression system ofclaim
 3. 5. The host cell of claim 4, wherein said expression systemencodes a polyprotein of at least about eight amino acids in length. 6.A polynucleotide probe comprising a sequence of at least 714 contiguousnucleotides, wherein said sequence selectively hybridizes to a genome ofhepatitis GB virus (HGBV) or its full complement, wherein said HGBVgenome encodes a polypeptide, wherein said polypeptide consistsessentially of an amino acid sequence, at least 48% identical to thepolypeptide sequence SEQ ID NO:387.
 7. A method for producing apolypeptide containing at least one hepatitis GB virus (HGBV) epitopecomprising the step of incubating host cells transformed with anexpression vector for a time and under conditions sufficient forexpression of said polypeptide, wherein said expression vector comprisessaid polynucleotide sequence of claim
 1. 8. The purified polynucleotideof claim 1 wherein said purified polynucleotide is at least 10nucleotides.
 9. The purified polynucleotide of claim 8 wherein saidpurified polynucleotide is at least 15 nucleotides.
 10. The purifiedpolynucleotide of claim 2 wherein said purified polynucleotide is atleast 10 nucleotides.
 11. The purified polynucleotide of claim 10wherein said purified polynucleotide is at least 15 nucleotides.
 12. Themethod of claim 7 wherein said purified polynucleotide is at least 225nucleotides.
 13. The method of claim 12 wherein said purifiedpolynucleotide is at least 327 nucleotides.
 14. A purifiedpolynucleotide comprising at least 15 nucleotides, isolated from apositive stranded RNA HGBV genome, wherein said genome encodes apolypeptide which consists essentially of an amino acid sequence atleast 51% identical to the polypeptide sequence SEQ ID NO:394.
 15. Anexpression system comprising said purified polynucleotide of claim 14,wherein said polynucleotide is operably linked to a control sequence.16. A synthetic or recombinant HGBV polynucleotide comprising at least15 nucleotides, wherein said polynucleotide encodes a polypeptide whichconsists essentially of an amino acid sequence, at least 51% identicalto the polypeptide sequence SEQ ID NO:394.
 17. A polynucleotide probecomprising a nucleotide sequence of at least 15 nucleotides, whereinsaid sequence selectively hybridizes to a genome of hepatitis GB virus(HGBV) or its full complement, wherein said HGBV genome encodes apolypeptide, wherein said polypeptide consists essentially of an aminoacid sequence, at least 51% identical to the polypeptide sequence SEQ IDNO:394.
 18. A method for producing a polypeptide containing at least onehepatitis GB virus (HGBV) epitope comprising the step of incubating hostcells transformed with an expression vector for a time and underconditions sufficient for expression of said polypeptide, wherein saidexpression vector comprises a HGBV nucleotide sequence of at least 15contiguous nucleotides isolated from a positive stranded HGBV RNAgenome, wherein said genome encodes a polypeptide, wherein saidpolypeptide has an amino acid sequence, at least 51% identical to thepolypeptide sequence SEQ ID NO:394.